Caret Tutorial – the Basics

·        Caret 5.5 Brain-mapping software

·        PALS Human Cortical Atlas

·        Macaque atlas; Monkey-human comparisons

·        SumsDB database, WebCaret visualization

 

22 September 2006

 

David C. Van Essen, John Harwell,

Donna Dierker, James Dickson, and Erin Reid

Washington University School of Medicine

Department of Anatomy and Neurobiology

St. Louis, Missouri USA 63110

 

 

 

            


Table of Contents

Introduction................................................................................................................................. 5

Part 1.  General Orientation to Caret and the PALS Atlas............................................................. 6

1.1 Launching Caret 5 (Linux, Mac, Windows)................................................................................................................. 6

1.2 Specification files (project-specific file listings)......................................................................................................... 6

1.2.1 Viewing file metadata.................................................................................................................................................... 7

1.2.2 Deleting spec file listings.............................................................................................................................................. 7

1.3 Loading data files............................................................................................................................................................ 7

1.4 Menubar, Toolbar, Display Control Locations........................................................................................................... 8

1.5 Menu bar overview......................................................................................................................................................... 8

1.5.1 Caret Preferences; Setting background and foreground colors................................................................................... 8

1.5.2 Caret Help.................................................................................................................................................................... 8

1.5.3 Caret Tips..................................................................................................................................................................... 9

1.5.4 Tutorial access via Caret Help..................................................................................................................................... 9

1.5.5 Menu popup (shortcuts)............................................................................................................................................... 9

1.6 Toolbar; standard views; rotation, zoom, pan............................................................................................................ 9

1.7 Display control (D/C) dialog.......................................................................................................................................... 10

1.7.1 The non-cortical medial wall........................................................................................................................................ 10

1.7.2 Medial Wall override.................................................................................................................................................... 10

1.8 View currently loaded files............................................................................................................................................. 10

1.9 Switching surface models.............................................................................................................................................. 10

1.9.1 Loading additional surface models.............................................................................................................................. 11

1.10 Multiple viewing windows........................................................................................................................................... 11

1.10.1 Yoking movements across windows........................................................................................................................... 11

1.11 Creating a scene............................................................................................................................................................ 11

1.12 Viewing surfaces and volumes concurrently............................................................................................................ 12

1.13 Viewing surface contours in volume slices............................................................................................................... 12

1.14 Surface shape files and columns................................................................................................................................. 13

1.14.1 Average sulcal depth.................................................................................................................................................. 13

1.14.2 Depth variability......................................................................................................................................................... 14

1.14.3 3D variability and variability spheres........................................................................................................................ 14

1.15 Topology files: closed, open, and cut........................................................................................................................ 15

1.15.1 Open topology............................................................................................................................................................ 15

1.15.2 Lobar cut topology and flat map................................................................................................................................ 15

1.15.3. Viewing nodes and links............................................................................................................................................ 16

1.16 Paint files and area color files...................................................................................................................................... 16

1.16.1 Paint color key display; highlighting locations and linking to ‘vocabulary’ files....................................................... 17

1.16.2 Changing Area colors................................................................................................................................................ 17

1.17 Probabilistic sulcal identification – surface and volume probabilistic atlas files................................................ 17

1.18 Paint files: cortical areas............................................................................................................................................... 18

1.18.1 Identify window – controlling displayed information.................................................................................................. 19

1.18.2 Column-specific comments......................................................................................................................................... 19

1.19 Border projection files and areal boundaries............................................................................................................ 20

1.19.1 Controlling border appearance.................................................................................................................................. 20

1.19.2 Border Color key display........................................................................................................................................... 20

1.20 Sterotaxic coordinates.................................................................................................................................................. 21

1.20.1 Latitude-longitude (LatLon) files................................................................................................................................ 21

1.20.2 Latitude-Longitude isocontours.................................................................................................................................. 21

1.21 Areal estimation files (fuzzy transitions)................................................................................................................... 22

1.22 Metric files (surface & volume)................................................................................................................................... 22

1.22.1 Probabilistic architectonic areas................................................................................................................................ 22

1.22.2 Viewing fMRI data – Functional Volume and metric files........................................................................................... 24

1.22.3 Viewing fMRI activations in relation to other experimental data................................................................................ 26

1.22.4. Mapping fMRI data................................................................................................................................................... 27

1.23 Foci and Foci projection files; Stereotaxic Neuroimaging Foci.............................................................................. 27

1.23.1 Foci Color Key........................................................................................................................................................... 28

1.23.2 Projecting foci............................................................................................................................................................. 28

1.23.3 Selective visualization of foci and metadata............................................................................................................... 28

1.23.4 Reporting coordinates in multiple stereotaxic spaces................................................................................................. 29

1.23.5 Selective viewing by foci color and class.................................................................................................................... 29

1.23.6 Viewing bilateral vs. unilateral foci............................................................................................................................ 29

1.23.7 Selective deletion and regrouping of foci.................................................................................................................... 29

1.24.8 Exporting Foci to spreadsheets.................................................................................................................................. 30

1.24 Viewing & editing text files.......................................................................................................................................... 30

1.25 Standard scenes for ongoing analyses...................................................................................................................... 30

1.26 Customizing your own PALS scenes and spec files................................................................................................ 31

1.27 Uploading data to SumsDB......................................................................................................................................... 31

1.28 Viewing multiple spec files concurrently................................................................................................................... 31

1.29 PALS left hemisphere analysis data set..................................................................................................................... 32

1.30 Concurrent viewing of left and right hemispheres................................................................................................... 32

1.31 Automatic hemisphere-specific data displays.......................................................................................................... 33

1.32 Individual Surface-specific data displays.................................................................................................................. 33

1.32.1 Left-Right Asymmetries............................................................................................................................................... 34

1.32.2 Viewing probabilistic maps bilaterally....................................................................................................................... 35

1.32.3 Viewing surfaces and volumes bilaterally.................................................................................................................. 35

1.32.3 Viewing neuroimaging foci bilaterally........................................................................................................................ 36

1.32.4 Standard –scenes for bilateral viewing...................................................................................................................... 36

132.5 Scenes for stereotaxic foci analysis.............................................................................................................................. 36

Part 2. SumsDB and WebCaret................................................................................................... 38

2.1 Overview........................................................................................................................................................................... 38

2.2 Getting Started in SumsDB............................................................................................................................................ 39

2.3 SumsDB Menu bar overview......................................................................................................................................... 39

2.3.1 Useful links................................................................................................................................................................... 39

2.4 WebCaret Demo.............................................................................................................................................................. 39

2.4.1 WebCaret MenuBar...................................................................................................................................................... 39

2.4.2. WebCaret Toolbar: standard views, rotation, zoom................................................................................................... 40

2.4.3 Scene selection.............................................................................................................................................................. 40

2.4.4 Display Control (D/C) Window.................................................................................................................................... 41

2.4.5 Popup block?................................................................................................................................................................ 41

2.5 Additional WebCaret atlas demo’s.............................................................................................................................. 42

2.6 SumsDB archive overview............................................................................................................................................. 42

2.7 Navigating directories and archives............................................................................................................................. 42

2.7.1 Spec files in Sums DB................................................................................................................................................... 42

2.7.2 Viewing spec file listings............................................................................................................................................... 43

2.7.3 Downloading checked files........................................................................................................................................... 43

2.7.4 Viewing file details........................................................................................................................................................ 44

2.8 Downloading commonly used atlas data sets............................................................................................................ 44

2.9 Publication-related data sets......................................................................................................................................... 44

2.10 Viewing published data and linking to online journals/figures.............................................................................. 44

2.11 Analyses using the Display Control window of currently loaded data................................................................ 45

2.12 Database ROI analyses................................................................................................................................................ 46

2.13 Format of ROI Search Results..................................................................................................................................... 47

2.14 Importing Search Results into WebCaret.................................................................................................................. 47

2.15 Local ROI analyses....................................................................................................................................................... 48

2.16 De novo ROI searches in SumsDB using a standard atlas template..................................................................... 48

2.16.1 Database ROI Search (fMRI data in metric file columns).......................................................................................... 48

2.16.2 Using ‘Show Nodes’ to view ROI results................................................................................................................... 49

2.17 Foci Searches................................................................................................................................................................. 50

2.17.1 Foci Study Searches.................................................................................................................................................... 50

2.17.2 Foci Data Searches.................................................................................................................................................... 50

2.18 Viewing FreeSurfer files converted to Caret.............................................................................................................. 51

2.18.1 Converting FreeSurfer files to Caret format.............................................................................................................. 52

2.19 Accessing SumsDB via online journal articles......................................................................................................... 52

2.20 Basic Archive Search.................................................................................................................................................... 52

2.21 Tutorial datasets and documents............................................................................................................................... 53

2.22 Options requiring logon............................................................................................................................................... 53

2.22.1 Navigating private datasets........................................................................................................................................ 53

2.22.2 Uploading data........................................................................................................................................................... 53

2.22.3 Code Access Agreement (CAA) and HiPAA constraints............................................................................................. 53

2.23 Establishing a local SumsDB server........................................................................................................................... 53

Part 3. Macaque Atlases (‘F99’, ‘F6’ and ‘PHT’) and Monkey-Human Comparisons.................. 54

3.1 Macaque Geography...................................................................................................................................................... 54

3.2 Cortical areas and functionally specialized regions................................................................................................... 55

3.3 Probabilistic maps and fuzzy transitions..................................................................................................................... 56

3.4 Viewing connectivity data............................................................................................................................................. 57

3.5 Monkey fMRI data.......................................................................................................................................................... 58

3.6 Spherical coordinates and multiple stereotaxic spaces............................................................................................. 58

3.6.1 Macaque F6 atlas......................................................................................................................................................... 58

3.6.2  Comparing the F99, F6, and PHT00 macaque atlas surfaces.................................................................................... 59

3.6.3  Standard scenes for ongoing analyses........................................................................................................................ 59

3.7 Left hemisphere and dual-hemisphere data sets........................................................................................................ 59

3.7.1 Standard scenes for left hemisphere............................................................................................................................. 60

3.7.2 Standard scenes for concurrent viewing of both hemispheres..................................................................................... 60

Part 4. Macaque-Human comparisons.......................................................................................... 61

4.1 Concurrent viewing of macaque, human surfaces (pre-registration)...................................................................... 61

4.2 Quantifying human-macaque cortical expansion ratios............................................................................................ 63

4.3 Evaluation of registration using fMRI data................................................................................................................. 63

4.4 Improved registration landmarks.................................................................................................................................. 64

4.5 Interspecies interpolation – ‘movies’ of human-macaque warping......................................................................... 64

4.6 Comparing deformed macaque orbitofrontal areas to human orbitofrontal areas................................................. 65

4.7. Spec files for Routine Analyses................................................................................................................................... 66

Part 5: Specific/selected analysis procedures................................................................................. 67

5.1 Mapping fMRI volume data – Average Fiducial and Multi-Fiducial Mapping..................................................... 67

5.1.1 Making a project-specific spec file................................................................................................................................ 67

5.1.2 Mapping multiple volumes onto both hemisphere surfaces.......................................................................................... 67

5.1.3 Viewing fMRI mapping results..................................................................................................................................... 68

5.1.4 Uploading mapping results to SumsDB....................................................................................................................... 69

5.1.5 Going public................................................................................................................................................................. 69

5.1.6 Command-line fMRI mapping...................................................................................................................................... 69

5.2 Mapping Stereotaxic Foci in Caret................................................................................................................................ 69

5.2.1 Making a project-specific spec file................................................................................................................................ 69

5.2.2 Mapping individual foci to the PALS atlas surface....................................................................................................... 70

5.2.4 Adding study metadata to a foci file.............................................................................................................................. 71

5.3 Batch processing -  from online journal tables to Caret foci via Excel.................................................................... 71

5.3.1 Copying online data into an Excel spreadsheet............................................................................................................ 71

5.3.2 Generating a Caret-compatible spreadsheet................................................................................................................ 72

5.3.3 Viewing the foci file in Caret......................................................................................................................................... 74

5.3.4 Generating a  foci color file.......................................................................................................................................... 75

5.3.5 Projecting foci............................................................................................................................................................... 75

5.3.6 Going public................................................................................................................................................................. 75

Appendix I. Downloading and installing Caret 5.3......................................................................... 77

 

 

Acknowledgments:

We thank numerous colleagues who have provided valuable suggestions for improving the PALS-B12 data sets and the Caret visualization and analysis methods.  Thanks also to Susan Danker for excellent efforts in text preparation. This project was supported by NIH Research Grant R01-MH-60974, funded  by the National Institute of Mental Health, the National Institute for  Biomedical Imaging and Bioengineering, and the National Science  Foundation.

 

 

Copyright 2006 Washington University

Permission to use, copy, modify, and distribute this document solely for non-commercial applications is hereby granted by Washington University free of charge, provided that the copyright notice "Copyright 2006 Washington University" appears on all copies of the software and that this permission notice appears in all supporting documentation. The name of Washington University or of any of its employees may not be used in advertising or publicity pertaining to the software without obtaining prior written permission from Washington University.

 

Washington University makes no representation about the suitability of this software for any purpose. It is provided "as is" without any express or implied warranty.

 


Introduction

 

Caret (Computerized Anatomical Reconstruction and Editing Toolkit) is a software application developed by the Van Essen lab for a variety of brain-mapping and neuroimaging purposes.  This tutorial aims to help beginning as well as more experienced Caret users in navigating (i) Caret 5.5 (September 2006 release); (ii) the PALS human cortical atlas and the macaque F99UA1 and F6 atlases; and (iii) the SumsDB database and its associated WebCaret visualization software. 

The tutorial contains five main sections in addition to this introduction.

PART 1.  Navigating Caret 5.5 (with many new features) and the PALS human cortical atlas.

PART 2.  Navigating SumsDB and WebCaret – visualization and search

PART 3.  Macaque surface-based atlases (F99, F6, and Paxinos = PHT00)

PART 4.  Monkey-human comparisons.

PART 5.  Selected Analysis Options (Map fMRI volumes to surfaces; Map stereotaxic foci)

Collectively, these serve a dual purpose:

-   a tutorial that can be used independently on your own time.   Each section can be navigated without having completed preceding sections, by starting from the appropriate ‘scene’.

-   a reference document, accessible online as well as within Caret (via the Caret Help menu).

Conventions – Tutorial text.  Awareness of the following conventions will facilitate navigation of this tutorial.

Non-bulleted, indented sections provide clarification and optional additional information, but are not essential for completing the action steps of the tutorial.

Access to data sets.  This self-guiding tutorial document and the associated data sets are freely available in SumsDB (http://sumsdb.wustl.edu/sums/directory.do?id=6585200; CARET_TUTORIAL_Sept-06/ in the Tutorials directory).  Download the pdf file (CARET_TUTORIAL_Sept06.pdf) and the data set (CARET_TUTORIAL_Sept06.zip).

Downloading and installing Caret software. If Caret 5.5 is not already installed on your computer, follow the instructions in Appendix I.

Additional Caret TutorialsThere are numerous capabilities in Caret 5 for analyzing surface and volume data and for mapping data from volumes to surfaces (and vice versa).  Currently, the best single source for these processing steps is the Caret 5 User’s Guide to Analysis Procedures, which is accessible from within Caret (Section 1.5.4).

Citing atlas and software. If you publish or give scientific presentations on work that capitalizes on Caret, SumsDB, and/or the associated atlas data, please give appropriate acknowledgment (http://sumsDb.wustl.edu/sums//html/links/citing.html).

Important note to current users of Caret and the human PALS and macaque F99UA1 atlases.  Many things have changed in this tutorial and the associated data sets since the previous release in June, 2006. We strongly recommend reviewing this tutorial so that you are familiar with the advantages of Caret 5.5 software and the associated data sets.  A list of recent changes to the atlas datasets is given in http://sumsDb.wustl.edu/sums/html/links/atlasdata.

Suggestions welcome! Corrections, bug reports, request for additional explanations etc. should be sent to the Caret-Users mailing list.  For details, see http://brainvis.wustl.edu/mailman/listinfo/caret-users.


 

Part 1.  General Orientation to Caret and the PALS Atlas.

Part 1 deals with data visualization and navigation in Caret. Caret has numerous options for analyzing data and modifying data files, some of which are described in Part 4.

Specific Objectives:

- Learn the basics of navigating Caret

- View the PALS atlas surfaces and volumes in Caret;

- View a associated data sets that are useful for a variety of analyses and comparisons

1.1 Launching Caret 5 (Linux, Mac, Windows)

Linux users:

Macintosh users:

Microsoft Windows users:

·                     If Caret5 aborts immediately with a message like “unable to find DLL OpenGL32.dll” go to the previous section of this document OpenGL Libraries for Microsoft Windows.

For those who run Caret5 from the command line, several options may be added to the command.  To see the options, add “  -help” to the command when starting Caret5 (“caret5  -help“ – note space between “caret5” and “-help”).

1.2 Specification files (project-specific file listings).          

There are seven specification files in this directory. Two are ‘DEMO’ spec files, with scenes customized for learning key steps in this tutorial, four are ‘STANDARD-SCENE’ spec files, which contain portfolios of scenes and associated data that can be useful for ongoing analyses and one is customized for stereotaxic foci.

Each specification (‘spec’) file contains a list of Caret-readable files, organized into nine major file types and even more subtypes.  A given spec file may list only a few files or many dozens of files, depending on the nature of the analyses the spec file is used for. 

Coordinate files specify the 3D location of each surface node.  Topology files specify how the surface is ‘tiled’ into a triangulated mesh.  (In most other surface visualization software, topology and coordinate data are stored together in a single file type, but keeping them separate in Caret has several practical advantages.)   All PALS_B12 surfaces are ‘standard-mesh’ representations (Saad et al., 2004) containing 73,730 nodes; hence the ‘surface-family’ number of 73730 in many file names.

1.2.1 Viewing file metadata

This surface is a population average of 12 individual right hemispheres.

A few files are checked by default (e.g., the most recent CLOSED and CUT topology files and the most recent FIDUCIAL, and FLAT coordinate files).

1.2.2 Deleting spec file listings

All files that are de-selected (grayed out) will be delete from the spec file listing once the spec file is loaded or the spec file window is closed.  This process will not delete the actual file within the current directory! 

Judicious use of this deletion option is important for good spec file management in projects that involve generation of various intermediate files.

                        This tutorial will familiarize you with (i) types of information contained in each major file type and (ii) ways to view each type of data in isolation or in various combinations.

1.3 Loading data files.

Caret provides two ways to start the data visualization ball rolling.  (i) Pressing the Load button (bottom left of spec file window) loads whatever files are currently checked.  (ii) Pressing the Load Scene(s) button loads only the scene file(s) listed in the spec file.   Typically, the Load Scene(s) option is a faster and easier way to start if  a pre-existing scene file is available.  

After several seconds (while the data are loaded), a lateral view of the PALS-B12 right hemisphere inflated surface will appear (Fig. 1.2).

The inflated PALS surface is a useful configuration for viewing many types of data, because it is smooth enough to make most regions visible yet retains enough convolutions to allow easy orientation to major geographic regions.

The surface coloration represents a map of ‘average sulcal depth’, in which darker regions are deeper below the cortical surface.

1.4 Menubar, Toolbar, Display Control Locations

Options for controlling what is displayed are distributed across three locations (Fig. 1.2)

- The ‘Menu bar’ at the top of the Main Window (top of the computer screen on Mac) has various pulldown menus.

- The ‘Toolbar’ just below the Menu bar (top of the main Caret window on Mac) has buttons for commonly used operations.

- The Display Control (D/C) window has multiple ‘pages’ that are selected using the ‘page selection’ pulldown menu.

The default is the scene’ page if you started by loading a scene file.

Text Box:  1.5 Menu bar overview.

The menu bar provides access to a wide variety of visualization and analysis options in Caret. 

§         Click on the Menu bar, then scroll the cursor over the various entries to see the pulldown menu associated with each option and submenu.   The functionality of some options is reasonably self-explanatory, but others are less obvious.

1.5.1 Caret Preferences; Setting background and foreground colors

·         Select File: Preferences to see the Caret Preferences window

·         Set Surface Background Color to 255 for the first of the ‘R, G, B’ entries

·         Press Caret Preferences: Apply to change the background color to red.

·         Restore the background color to black (0, 0, 0) and press Apply.

Alternatively, if you prefer a white background, set the background to (255, 255, 255) and set the foreground to black (0, 0, 0) or some other color so that you can read text displays (.e.g., volume coordinates)

Note that there are various other options available in the Preferences menu.

Fig. 1.3  Caret Help Menu

 
1.5.2 Caret Help

§         Select Menu bar: Help: Caret Help to open the Caret Help window (Fig. 1.3A).

The Help Menu provides information and instructions regarding many Caret functions, not all of which are discussed in this tutorial.

§         Click the marker to the left of the Help Page Index: Menus.

§         Select Help Page Index: Menus: File for a description of each option in the File category. 

§         Expand the Caret Help window (drag the lower right corner) as in Fig. 1.3B.

§         Select Help Page Index: Menus: Attributes for a description of each submenu (area colors, etc.) followed by longer descriptions of each submenu option.

Fig. 1.3 Caret Help Menu

 
Detailed instructions are provided for some of the more complex operations (e.g., statistical analyses), so the Help menu is a useful ‘go-to’ place when questions arise.

§         Click the arrow next to Help Page Index: Toolbars.

§         Select: Help Page Index: Toolbars: Toolbar Main Window for a description of each button and pulldown menu function.

1.5.3 Caret Tips

If Show Tips After First Spec File Loaded is checked, the Caret Tips window will appear each time you launch Caret.   Otherwise, Caret Tips can be accessed from the Help menu.

Note that Show Tips after First Spec File Loaded provides the option to receive tips regularly, each time you launch Caret.

1.5.4 Tutorial access via Caret Help.

§         Press Help Page Index: Caret 5.5 Tutorial to see the pdf version of this tutorial. Expand the Caret Help Window size for easier reading.

§         Press Help Page Index: Caret Analysis Tips. Currently, this shows a pdf of the Caret 5 User’s Manual and Tutorial (March 2005, Caret Version 5.2).  This manual includes instructions for many data analysis and processing steps (e.g., mapping fMRI volumes onto surfaces; mapping stereotaxic foci onto surfaces).

              - This document has some redundancy with the current (Caret 5.5) tutorial.

              - Analysis capabilities introduced since March 2005 are not covered.

              - A few analysis steps described for Caret 5.2 work differently in Caret 5.5.

    This document will be revised and updated in a future Caret release.

§         Close the Caret5 Help window to reduce clutter.

1.5.5 Menu popup (shortcuts)

§         Press  the right mouse button (Ctrl Click on the Mac) to see a popup set of menu shortcuts (Fig. 1.3C).  Suggestions for when to use various of theses options are scattered throughout the tutorial.

1.6 Toolbar; standard views; rotation, zoom, pan.

§         Place the mouse cursor over Toolbar: D (but don’t press the button yet).  A popup description of the button’s function will appear (‘Switch to Dorsal View of Surface’).

§         Now press Toolbar: D for a dorsal view.

‘M, L, A, P, D, and V’ buttons provide standard views.  ‘R’ resets to the default dorsal view.  ‘X, Y, and Z’ rotate by 90 degrees around the screen x, y, and z axes, respectively.

§         Rotate the surface freely by placing the cursor in the Caret main window and moving the mouse with the left cursor button depressed (main button on a single-button mouse). 

§         In the Toolbar: axis selection pulldown menu (just left of the D/C button; current reading ‘XY’), select Axis Selection: Y and observe that the free rotation is now constrained to rotation about the screen Y axis.

§         Pan the surface using the Shift left button (Shift-click for Mac/single-button mouse).

§         Zoom the surface using the Ctrl-left-click button (-click for Mac/single-button mouse).

§         Press Toolbar: R to reset the surface to the default dorsal view.

§         Select Toolbar: XY from the axis selection pulldown menu to restore free rotation about the x and y axes.

§         Press Toolbar: M for a medial view of the atlas surface.

§         Note that the non-cortical regions along the medial wall appears black.

1.7 Display control (D/C) dialog

§         Press the Display Control: Page Selection pulldown menu and note that five pages are available for selection.

The number of available pages depends on the number of file types currently loaded.

§         Select Display Control: Page Selection Overlay/Underlay – Surface.  This page provides various options for controlling what is viewed as a primary (topmost) overlay and as secondary (‘underneath’) underlay

Note that ‘Paint’ is selected as the primary overlay, and ‘Shape’ as the Underlay. (There is also a secondary overlay option, but nothing has been selected for it.)

    See the User’s Guide (pp. 7-9) for additional explanation of the D/C dialog

1.7.1 The non-cortical medial wall

§         Press the Primary Overlay: No Coloring button, and note that the non-cortical medial wall shading changes from black (painted) to a yellow-brown color (unpainted, dictated by the selected shape column). Then press the Primary Overlay: Paint button to restore the black medial wall.

This display of the PALS inflated surface is topologically ‘closed’ – i.e., an explicit surface spans the non-cortical medial wall region.  A general recommendation is to ‘hide’ the non-cortical medial wall by painting it black (as done here), thereby making it easy to discern the natural termination of cortex.

1.7.2 Medial Wall override.

A more flexible way of painting the medial wall black is to use the Medial Wall override option.

·         Press Primary Overlay: No coloring, so that the medial wall is not painted black.

·         Select Page Selection: Paint

·         Press the Enable Medial Wall Override button and select AVERAGE-MED-WALL B1-12 RIGHT in the Medial Wall Override pulldown menu.

This will ensure that the medial wall is painted black irrespective of what other overlay/underlay selections are made. It is a useful default mode for most visualization purposes. (The color is specified in the ‘area color’ file and can be adjusted using the Attributes: Area Colors:Edit option.)

·         Select Page Selection: Overlay/Underlay – Surfaces

·         Press Primary Overlay: Paint

·         Press the Paint column selection menu (which currently displays ‘AVERAGE-MED-WALL B1-12 RIGHT’ column) and select the Lobes column to view a display of cortical lobes in different pastel shades. 

Switching among various columns in the currently loaded paint file can be done using the pulldown paint menu  shown here, but more conveniently in a separate paint selection page that is demonstrated in Sections 1.16 and 1.17.

·         Press Primary Overlay: No coloring to restore the average sulcal depth map

1.8 View currently loaded files.

§         Press File: View Current Files to see what files are currently loaded in Caret.

      Two topology files and two coordinate files are currently loaded, plus 6 other files (based on the files listed in Scene 1).

Any of the currently loaded files can be deleted from Caret’s working memory by pressing the ‘X’ button alongside each file (in the ‘clear’ column).

§         Close the  View Current Files window

1.9 Switching surface models.

Any number of coordinate and topology files can be loaded concurrently in Caret, as long as they have the same number of nodes (i.e., belong in the same ‘surface family’, like the 73,730-node PALS surfaces).

§         Select the Toolbar: Model: FLAT surface model (configuration) from the pulldown menu (current listing: INFLATED) to see the PALS atlas flat map. 

Caret assigns the CUT topology to the FLAT coordinate file and the CLOSED topology to the INFLATED coordinate file based on assignments specified in the coordinate file metadata. 

File name changes. The PALS left and right hemisphere flat maps are identical to those originally published (Van Essen, 2005a) but for conciseness and clarity have been given shorter file names (omitting reference to the ‘colin’ surface where their shape was originally created.)

1.9.1 Loading additional surface models

§         Press Toolbar: Spec to bring up the spec file listing.

§         Press the Specification File: Coordinate File: VERY INFLATED open button (3rd from bottom of coordinate file list) to load the PALS Very Inflated surface.  It will be appended to the already loaded coordinate files.

§         Select File: Open Data File, select File Type: Coordinate File

                  This provides access to all files in the current directory, not all of which are listed in the spec file.

§         Select the first of the . . . RIGHT. . . FIDUCIAL . . . coord files to view the average fiducial surface in ‘711-2C’ space (see Section 1.24.4).

§         Click the right mouse button (Ctrl-Click on Mac) and select Show brain model: FLAT to restore the flat map view using the menu popup mode.

1.10 Multiple viewing windows.

It is often convenient to view multiple surface configurations concurrently.

§         Select Menu Bar: Window: Window 2 to bring up an additional viewing window.

Note the shortcut to opening new windows (2,  3, etc. for Mac; Ctrl1, Ctrl2 etc. for PC) indicated in the pulldown windows menu.

1.10.1 Yoking movements across windows

§         Expand Window 2 so it is comparable in size to the main window (by dragging the lower right corner).

§         Select Window 2: Model: VERY INFLATED for a default view of the very inflated surface.

§         Press Window 2: Yoke (on the far right, sometimes hidden if the window is small.

§         Rotate, pan, and zoom (as in Section 1.6) the surface with the cursor in either window, and note how the surface movements are yoked.

§         Press Window 2: Toolbar: Yoke again to de-select yoking.

§         Text Box: Fig. 1.4. A scene with multiple viewing windowsResize Window 2 to be much smaller, as in Fig. 1.4

§         Press 3 (Mac) or Ctrl3 (PC) to bring up a third viewing window more quickly and conveniently.

§         Drag Window 3 directly below Window 2 and move the Display Control window to the right of the these windows.

§         Select the FLAT model in the Main Window, the INFLATED model in Window 2, and the VERY INFLATED model in Window 3

§         Press Toolbar: L in Windows 2 and 3 for lateral views of the inflated models.

§         Place the cursor in Window 2 and zoom the surface to fill the window.  Do the same for Window 3 (Fig.1.4)

1.11 Creating a scene.

The combination of surface models and viewing windows you just generated (Fig. 1.4) is handy for viewing many kinds of experimental data.  While it is important to have learned these steps, it is tedious to recreate this and similar ‘scenes’ from scratch, owing to the number of discrete operations required.  Fortunately, such tedium can be bypassed by saving the current ‘state’ of Caret as a scene within a scene file.  The scene can later be regenerated by a single command.

§         Select Display Control: Page Selection: Scene, and highlight Scene 1 (but DON’T double-click on it).

§         Press Insert New Scene.

§         Enter Flat, Inflated, very Inflated (PALS-B12 RIGHT)  in the popup window.

§         Select File: Save Data File: Scene File.

§         Press the Save button and press Yes on the Replace query button to overwrite the current scene file.

Note the options to include comments describing the saved file and to assign it a different file name.

·         Press Display Control: Scenes: Unload All Files Except Scene, then press Yes in the popup query window to delete the currently loaded files from working memory.

·         Select (double-click) Scene: Flat, Inflated, very Inflated (PALS-B12 RIGHT) to convince yourself that the just-saved scene can be immediately and completely restored.

1.12 Viewing surfaces and volumes concurrently. 

It is often desirable to view the PALS atlas surfaces in conjunction with the atlas structural MRI volume.

§         Select Scene 2 Inflated, Avg Fiducial, Avg MRI (PALS RIGHT) from the Display Control: Scene listing.

     The main window shows the PALS inflated surface; Viewing Window 2 shows the ‘average fiducial’ surface of the PALS right hemisphere. Viewing Window 3 shows a horizontal slice through the PALS average structural MRI volume (Fig. 1.5).

      The crosshairs in Window 3 are centered on the postcentral gyrus and correspond to the highlighted blue node in the surface views.

      The average fiducial surface and average MRI volume were generated from 12 individual subjects by a process discussed in Van Essen (2005a).

Text Box: Figure 1.5. Scene 2. Main window:  Lateral view of PALS inflated surface.  Window 2:  Lateral view of average fiducial surface.  Window 3:  Surface contours of Case 1 right hemisphere overlaid on structural MRI; fiducial and inflated surfaces (lateral views) with sulcal depth displayed.      In Window 3, the x, y, z slice plane (voxel) numbers (141, 107, 117) are expressed relative to an origin in the left, posterior, inferior (LPI) corner of the volume.

The cursor coordinates relative to the anatomical origin (the anterior commissure = AC) in ‘FLIRT’ stereotaxic space  are indicated in the lower left of the window (50, -19, 44).  See Section 1.24.4 for additional information on stereotaxic spaces.

§         In Window 3, use the arrow buttons to the right of the z slice level (starting value = 117) to scroll to different horizontal levels.

·         In Window 3, select Toolbar: C(XZ)  for a coronal view, then use the arrow keys next to the y slice level (starting value = 107) for different coronal levels.

·         Click on any location of interest in the Caret main window (e.g., on the precentral gyrus).  The selected node and the corresponding node in Window 2 will be highlighted by blue squares, and the cursors in Window 3 will jump to the corresponding location and slice level. 

·         Click on various locations in Window 2 and Window 3 to further explore the relationship between surface and volume representations in the PALS atlas.

   See User’s Guide (pp. 5-6, 11) for additional tips on volume visualization (e.g. oblique volume slices, montages).

1.13 Viewing surface contours in volume slices.

·         Select Display Control: Page Selection: Overlay-Underlay – Volume, then press the Settings tab.

The surface contour displayed on the volume slice is that of the PALS average fiducial surface. 

·         Select Surface Outline: Color: Red from the selected surface to change the color of the surface contour. 

Note that the surface slice thickness can be changed as well, and that other surfaces can be concurrently viewed as well, with independent control over their color assignments.

·         Select Display Control: Page Selection Scene, then double-click Scene 2 to restore the preceding scene. 

·         Select Toolbar: Model: VOLUME in the main window, then Toolbar: Volume Axis: All (current reading: H) to view the volume in all three standard planes.

·         Select Toolbar: Model: VERY INFLATED in Window 2, then Toolbar: L.

·         Select Toolbar: Model: FLAT in Window 3.

·         Resize the surfaces in Windows 2 and 3 (using the zoom option – Ctrl-left or -click) so they approximately match Fig. 1.6.

·         Click on various locations in any of the windows to further explore the relationships between surface and volume representations.

·         Press Identify Window: CID to erase the highlighted surface nodes.

·         In Window 2, Press Toolbar: M for a medial view of the very inflated surface, then click on various locations on the medial aspect of the hemisphere to see where the corresponding locations are on the flat map and in the volume slices.

·         (Optional) Insert and save  new scene: Enter MRI (3-slice view); Very Inflated, Flat (PALS-B12 RIGHT)  using the steps in Section 1.12.

The purpose of this (and later) optional exercises is to insure that you (i) remember how to create and save scenes, and (ii) get into good habits of saving scenes as a matter of routine practice.

1.14 Surface shape files and columns

Text Box: Figure 1.6.  Main window:   Multi-slice (parasagittal, coronal, horizontal)  average sMRI, with average fiducial surface contours overlaid. Windows 2 and 3:  Lateral view of very inflated PALS surface and flat map, with average sulcal depth displayed.The PALS atlas contains many types of experimental data that can be useful for a variety of visualization and analysis purposes.  This section shows how to view several types of information contained in ‘surface-shape’ files. In general, surface shape files encode real-valued (continuously varying) data related to cortical shape characteristics.

Each subsection starts with a pre-existing scene (generated by steps you should be familiar with), introduces new data files and representation options, and ends up with a new scene that you have the option to save, but is also accessible in a pre-existing standardized scene file that you may find useful in the future.

1.14.1 Average sulcal depth

·         Select Scene 3 (Flat, Inflated (lateral, medial)) for a map of average sulcal depth, displayed on the PALS flat map and inflated surface (Fig. 1.7).

·         Select Page Selection: Overlay/Underlay – Surfaces

In this starting configuration, the average sulcal depth is set as the underlay – i.e. as a standard background on which to view various other kinds of data. 

Text Box: Fig. 1.7. Scene 3. Flat + inflated (lateral, medial view)In the medial view (window 3), medial wall is black – again useful as a starting point.  The paint column is set as the primary overlay, so that the medial wall will ‘override’ other types of data.

·         Select Display Control: Page Selection: Surface Shape  

·         Press the Settings tab, then switch from Color mapping: gray to Orange-Yellow.

This conveys the same information as the gray-scale mapping, but more vividly.  Note that the depth range (Settings: Selected column: Mapping) is set at -30 to +10 mm; the negative maximum of -30 mm approximately matches the maximum depth (-32.9 mm) for this column.

·         Press the Selection tab, then select the low-contrast (LowContrast Average…) column.

The low-contrast sulcal depth map is often useful when preparing illustrations, because it portrays underlying geography as a subtle background, allowing overlying experimental data to appear more prominently.

·         Select the Settings tab.  Note that the depth range (Settings: Selected column: Mapping) from -60 to +20 mm instead of the default -30 to +10 mm. You can make additional adjustments yourself.

1.14.2 Depth variability. 

Because the PALS-B12 atlas is population-based, some shape characteristics can be characterized in terms of their variability as well as average value.

·         Press the Selection tab, then select the DEPTH VARIABILITY – DEPTHnr B1-12 RIGHT…) column. 

Terminological note on ‘columns’ vs ‘rows’.  In the Surface Shape Page Display window, the various ‘columns’ are arranged as ‘rows’ from top to bottom. The term ‘column’ is used because the text (ASCII) data files are organized with a variable number of columns reflecting the number of data values assigned to each of the 73, 730 surface nodes (rows).  The column terminology applies to various other file types, including paint and metric files.

·         Press Settings tab, then click on the Color Mapping: Palette button.

·         Select videen-style from the pulldown menu.

·         Press the Display Color Bar button to see the color scale in each window (Fig. 1.8).

Text Box: Fig. 1.8. Depth variability map.Depth variability is low (blue-gray) in most regions (signifying relatively consistent values across individuals after surface-based registration), but is high (green/yellow/red) in parietal, temporal, and frontal regions where shape variability is more pronounced.

1.14.3 3D variability and variability spheres.

·         Press the Selection tab, then select the 3D VARIABILITY – RIGHT Hem Human.PALS_B12 column.

·         In Viewing Window 3, select Model: FIDUCIAL…; press Toolbar: L in the same window, and resize the average fiducial surface to fill the window (as in Fig. 1. 9). 

3D variability is generally much larger than depth variability (Fig. 1.8 vs 1.9) for reasons explained elsewhere (Van Essen, 2005a).

·         Press the Settings tab, then check the Node ID Deviation box and select the 3D VARIABILITY – RIGHT Hem Human.PALS_B12 column.

·         Text Box: Fig. 1.9. 3D variability map plus variability spheres.Click on a few nodes at various locations, as in Fig. 1.9 and note that the size of the resultant spheres correlates with the 3D variability value.

The radius of the blue sphere in the average fiducial surface represents the magnitude of the 3-D variability at that location.  The size of the sphere is a measure of the variability in 3D location in the fiducial surfaces of a population of individuals. 

In the Identify Node window, the value for the 3rd and 4th columns represent 3D variability and depth variability, thus permitting easy comparison of their respective values for different nodes.

·         Press Identify Window: CID to clear the identified nodes from the display, and press Identify Window: Clear to clear the window contents.

·         Switch from Color mapping: palette back to Gray

·         Press the Selection tab and select the low-contrast (LowContrast Average…) column.

·         [Optional] Save this scene as: Flat, Inflated, Very Inflated (LowContrast; IDnode = 3D variability) PALS-B12 Right (as described in Section 1.11)

1.15 Topology files: closed, open, and cut

·            Select Page Control: Scene

·            Select Scene 4 (Very Inflated (Medial) flat) for a display used to illustrate how the choice of topology file affects the appearance of different surfaces.

1.15.1 Open topology

·            Press Toolbar: Spec and open the OPEN topology file.

·            Select Surface: Topology: Set Topology Assigned to Surfaces, then select the OPEN topology file for the VERY INFLATED surface.  The medial wall nodes will disappear, making the backside of temporal cortex visible. 

·         While looking through the medial wall hole, rock the very inflated surface back and forth to get a better appreciation of the 3D configuration when a medial wall hole is present.

Text Box: Fig. 1.10. Lobar cut and standard Caretesian flat maps with correct topology (cuts) in top row and incorrect topology in bottom row.In general, the OPEN topology is not good for visualization purposes (an opaque medial wall is better).  However, the open topology is quite useful for certain analyses  where it is useful to exclude medial wall nodes from selected surface-based analyses.

·            Select  Set Topology: CUT topo file for the very inflated surface.  Elongated cuts will now be visible in the occipital and parietal lobes.  These cuts are necessary for viewing the flat map properly, but are generally not useful for viewing or computing area, distances, etc. or 3D surfaces.

·            Click on nodes on opposite sides of the occipital cut in the very inflated view, and note how the highlighted nodes are far apart on the flat map.

1.15.2 Lobar cut topology and flat map

·         Press Toolbar: Spec and open the LOBAR cut coord file (scroll to the bottom of the coordinate file list).

This will load a flat map with a different set of cuts that run along the margins of the frontal and occipital lobes, rather than midway through them (Fig. 1.10).  A ‘lobar cut’ topology file is automatically loaded as well (because it is present in the directory and is specified in the coordinate file metadata).

·            In the Set Topology window, select the FLAT LOBAR flat map and switch from the default Lobar Cuts topo file to the Cartesian Standard topo file, and note how the flat map appears abnormal when the wrong cuts are applied.  Likewise, assign the lobar cuts to the Cartesian standard flat map (Fig. 1.10, lower panels).

·            Close the Set Topology window.

1.15.3. Viewing nodes and links

·            Select Scene 5 for a standard flatmap view.

·            Select Page Selection: Surface Miscellaneous

·            Select  Drawing Mode: Nodes

·         Zoom up on the flat map until you see the discrete nodes of the surface, as in Fig. 1.11C.

These are a few of the 73,730 nodes in the PALS standard-mesh surface. Each node’s position is encoded in the FLAT coordinate file.

Standard-mesh surface representations (Saad et al., 2004) have major advantages in facilitating concurrent visualization of different hemispheres (left and right atlas hemispheres; individual and atlas hemispheres, macaque and human hemispheres) as is demonstrated in subsequent sections.

·            Increase the node size to 6.0 (from the default of 2.0) using the arrow button so that the individual nodes are clearly visible.

·            Select Drawing Mode: Nodes and Links to view the links (Fig. 1.11D) that are specified in the topology file and form a ‘tessellation’ or triangulated mesh.

·            Press Toolbar: R to reset the size of the flat map

·            Text Box: Fig. 1.11.  Viewing nodes, links, and edges.Select Drawing Mode: Links (Edges only) to see just the edges associated with the cut topology file on the flat and very inflated surfaces (Fig. 1.11B).

1.16 Paint files and area color files.

Paint files are used to color surface nodes by assigning various nodes to paint ‘categories’.  The displayed color for each category is specified in a separate ‘area color’ file.  The initial example shows how paint and area color files are used to specify cortical geography (identified sulci). 

·         Select Page Selection: Scene, then press Unload All Files Except Scene.

·         Select Scene 6 Flat, inflated  (Lateral, medial); no paint or area colors (PALS-B12 Right) to view a flat map and lateral and medial views of the inflated surface (without the medial wall shaded).

·         Select Toolbar: Spec: Paint and de-select Auto Close

·         Open the one Area Color file (Human.Cerebral.COMPOSITE…) and press Replace.

·         Open the Human.PALS_B12.IDsulci_B1-12… paint file, and press OK on the Choose Columns to Load popup.

·         Close the Spec window.

·         Select Page Selection: Overlay/Underlay – Surface then press Primary Overlay: Paint

·         Select Page Selection: Paint

·         Select the def Buckner Case 1 column for a view of identified sulci in Case 1 after registration to the PALS-B12 atlas.

1.16.1 Paint color key display; highlighting locations and linking to ‘vocabulary’ files.

·         Press the Display Color Key on the Display Control: Paint page.

The popup Paint /Color Key shows the colors assigned to each of the sulci (Fig. 1.12). 

·         Press the purple color bar to the left of Paint Color Key SUL.AOS to highlight the surface nodes lying within the anterior occipital sulcus.

·         Click the SUL.AOS color bar again to toggle off the highlighting.

·         Press the color bars next to several other sulci to highlight them concurrently.

·         Press CID in the Identify Window to clear all of the highlighted nodes at once.

·         Text Box: Fig. 1.12. Identified sulci from Case 1, with Color Key displayedPress Paint Color Key: SUL.AOS (the text itself) and note that there is no information reported in the Identify Window.

This changes if an appropriate ‘vocabulary’ file is loaded.

·         Select Toolbar: Spec Misc and open the Human.Geography.vocabulary file, and press Replace in the popup window.

·         Press Paint Color Key: SUL.AOS (the text itself) again and note that the full name of the sulcus (Anterior Occipital Sulcus) is now reported in the Identify Window, along with a reference to the Ono et al. (1990) atlas used as a guide in identifying sulci.

The contents of a vocabulary file can be revised and expanded using the Attributes: Vocabulary: Edit option.

·         (Optional) Click on any other sulci whose full name and location you would like to see.

·         Select the second paint column to see the identified sulci of Case 2 registered to the PALS atlas.

·         Press Identify Window: CID to clear any highlighted nodes.

1.16.2 Changing Area colors

Some of the area colors may appear unaesthetic if not downright ugly to you. They are easy to change!

·         Select Attributes: Area Colors: Edit

·         Scroll down to the ‘SUL.*’ section and select SUL.OTS

·         Change the color using the color slider bar to . . .

·         Press Color File Editor: Apply

The color change will be evident in the Caret windows, but the Area Color File must be saved to preserve any changes

·         Press Color File Editor: Advanced Color Selection and note that there are various other ways to adjust area colors

·         Close the Advanced Color Selection and Color File Editor windows.

1.17 Probabilistic sulcal identification – surface and volume probabilistic atlas files.

Maps of identified sulci for all 12 right hemispheres can be viewed one at a time in the currently loaded paint file.  To obtain a probabilistic representation of these data, the same file can be loaded into Caret as a ‘probabilistic atlas’ file.

·         Press Toolbar: Spec.

·         Select Specification File: Paint: Probabilistic Atlas Files and press Open to load the Human.PALS_B12.IDsulci_B1-12_RIGHT.clean.73730.atlas.paint file. 

·         Select Page Selection: Overlay/Underlay – Surface.  

·         Press the Primary Overlay: Prob Atlas button.  The surfaces will now show a probabilistic map of identified sulci.

·         In the Identify Window, click on the lower-case ‘p’ button for reporting of probabilistic atlas data. 

·         Click on a node in the central sulcus (Fig. 1.13A, black arrow) and note that all (or nearly all) nodes are identified as SUL.CeS, signifying the consistency with which the central sulcus was aligned in the 12 subjects contributing to the PALS-B12 atlas.

·         Click on a node in the occipito-temporal cortex (Fig. 1.13A, red arrow) and note that many different geographic locations are reported (e.g., GYRAL, SUL.LOS, SUL.AOS, SUL.pITS), signifying that surface-based registration did not achieve precise alignment of sulci in regions of known high variability.

In general, surface-based registration achieves substantially better alignment of identified sulci than does volume-based registration throughout the cortex (see Fig. 8 and Table 1 in Van Essen, 2005a).

·         Select Page Selection: Probabilistic Atlas – Surface. 

There are a number of display options for adjusting how the probabilistic maps of sulcal identity are viewed (e.g., threshold ratio is the fraction of entries that must have the same assignment in order to appear above threshold).  Others are generally self-explanatory and are not considered further in this tutorial.

·         Press Identify Window: CID to clear the highlighted nodes.

·         Select Page Selection: Scene

·         Select Scene 7 for a view that includes the average structural MRI volume along with atlas surfaces displaying probabilistic sulci.

·         Select Toolbar: Spec: Volume: Volume Files – Prob atlas and open the PALS_B12.B1-12.BOTH-HEMS.PROB-ATLAS_IDsulci. . . file; press append.

·         Select Page Selection: Overlay/Underlay– Volume. 

·         Press the Primary Overlay: ProbAtlas button to see probabilistic sulci in the volume (Fig. 1.13).

·         (Optional) Save the scene as: Flat, Inflated (ID sulci) + Coronal MRI, IDsulci (PALS-B12).  

·         Press Page Selection: Scene: Unload all Files Except Scene and press yes on the popup.

   See User’s Guide, pp. 20-21 for instructions on mapping a painted surface to a paint volume.

1.18 Paint files: cortical areas

Multiple cortical partitioning schemes are currently available in the PALS atlas dataset.

·         Select Scene 8 Flat, inflated  (Lateral, medial); Lat-lon (PALS-B12 Right) to view a flat map plus lateral and medial views of the inflated surface with identified sulci loaded as a paint file (as in Fig. 1.12).

·         Select Toolbar: Spec: Paint and de-select Auto Close.

·         Open the Human.PALS_B12.BOTH.COMPOSITE… paint file.

·          Press Erase All Existing Columns, then press OK on the Choose Columns to Load popup.

The surfaces will now show a map of cortical lobes (first column in the newly loaded paint file) instead of Case 1 identified sulci.

·         Select Spec: Misc: Open Vocabulary Files: Human.CorticalAreas.vocabulary and press Append.

·         Close the spec window.

·         Press Paint Color Key: Update.

·         Select Page Selection: Overlay/Underlay– Surface.   

·         From the Paint pulldown menu, select the Geography – Colin RIGHT on PALS column for a view of buried cortex in the colin individual right hemisphere - the individual surface-based atlas (Van Essen 2002) that has been supplanted by the PALS-B12 atlas.

·         Return to the Lobes column.

·         Press Underlay: Geo Blend to see cortical geography (colin right hemisphere) underlying the lobes.

·         Increase the Geo Blend value from the default 0.6 to 0.9 to see a fainter representation of the background geography.

·         Select Page Selection: Paint

·         Select the Visuotopic column for a map of visuotopic areas revealed in fMRI studies.

·         Press Paint Color Key: Update

The popup Paint /Color Key will allow you to easily identify the different visual areas by their color.  This can be handy during figure generation

·         Press the Visuotopic.MTplus text on the Display Color Key to see the full name of this area displayed in the Identify Window, plus a link to the relevant online publication.

·         Press the red color bar to the left of Visuotopic.MTplus Display Color Key to highlight the surface nodes lying within MTplus.

·         (Optional) Click on any other visuotopic areas name or color bars you are interested in learning about.

1.18.1 Identify window – controlling displayed information

·         Click on one of the painted areas and note that only the node coordinates and the node number are reported in the Identify Window.

·         Press Identify Window: P (capital) to enable paint column information (it will turn gray), and press Identify Window C, (the rightmost ‘C’ for displaying coordinate information, not the leftmost ‘C’ for displaying ‘cell’ information).

·         Click on a painted area and note that the Identify window now reports information on that node for each of the loaded paint columns; the selected column (visuotopic) value is shown in bold font.

If you want all types of node information displayed, press Identify Window: All-N. However, this can sometimes cause more clutter than you want.

   See User’s Guide (p.10) for added tips on the Identify Window.

1.18.2 Column-specific comments

·         Press the ? button next to Visuotopic Both on the Display Control: Paint page for information about the studies contributing to this map.

For example, the visuotopic areas were mainly derived from the fMRI study of Hadjikhani et al, 1998, and there are hyperlinks to the PubMed abstract and directly to the online journal article. 

 

 

·         Press one of the links (e.g., doi: http://dx.doi.org/doi:10.1038/681) to launch a browser window that links directly to the publication on which these maps were based.

·         Press Close on the Comment Editor popup.

1.19 Border projection files and areal boundaries

·         Press Toolbar: Spec and uncheck the Auto Close button

·         Press Spec File: Border, and open the Human.Cerebral.Composite.border color file and press Append

·         Open the PALS_B12.LR.BOTH.COMPOSITE_AREAS.73730.borderproj file. and press Append.

·         Close the spec file window.

·         Select Page Selection: Border.

1.19.1 Controlling border appearance

·         From the border display pulldown (current listing: Draw Borders as Points) select Draw Borders as points and lines. Many ‘ectopic’ lines will appear that connect to borderpoints that projected to the origin because they lie over the cuts in the flat map.

·         Select Draw Borders and unstretched lines.

This will display each border as a continuous line but will avoid undesired links to border points located at the origin because they traverse cuts on the flat map.

1.19.2 Border Color key display

·         Press the Border: Main tab, then press the Display Color key button.

The selected borders all have the same color, but their names are listed separately.

·         Press the Brodmann 17 border color bar to see its location highlighted by increased thickness

·         Press the Border: Color Tab and note that the selections are grouped into broader categories (established by the names in the currently loaded border color file). 

·         Press the Border: Color: All Off button, then toggle the Brodmann borders on to see Brodmann areas overlaid on visuotopic areas.

·         Press the Brodmann 17 border color bar again to toggle off the highlighting

·         Click on various border names to see their full names in the Identify Window.

·         Click on a node in the red patch near a border to see that this is visuotopic area MT plus that lies near the border between Brodmann areas 19 and 37 (Fig. 1.14A.)

·         Select the Border: Color tab and toggle the Brodmann borders off and the visuotopic borders on to see that they indeed overlay the painted visuotopic map.

·         Select Page Selection: Paint and select the Brodmann column to see a complementary representation of the Brodmann and visuotopic area maps.

·         Press the Paint Color key: Update

·         Press Page Selection: Border: Main: Override Border Colors with Area Colors, and update the Display Color Key.

Brodmann areas and visuotopic areas are now displayed in independent sets of individually colored and labeled patterns.

·          Select Page Selection: Paint: Orbitofrontal for a map of orbitofrontal areas mapped from postmortem case Fb.L (Ongur et al.  2003), with a much finer-grained set of areas than in the Brodmann scheme (Fig. 1.14B).

This map of human orbitofrontal areas differs significantly from previously orbitofrontal maps (cf. Van Essen 2005c) and is more accurate (owing to improvements in surface-based registration from flat map via spherical registration).

·         Press Paint Color Key: Update.

·         Select the Williams Syndrome column and update the Paint Color Key to see the location of many distinct cortical folding abnormalities in the right hemisphere reported by Van Essen et al (2006). 

Blue and green regions are deeper on average in Williams Syndrome; red and yellow regions are deeper on average in controls.  For additional details about this study, press the query button and click on the direct link to the online publication.

   See User’s Guide (pp. 15-17) for instructions on how to draw open and closed borders and painting in closed borders.

Text Box: Fig. 1.14B. Orbitofrontal areas (Ongur et al., 2003) plus Brodmann areal boundaries               

Text Box: Fig. 1.14A. Visuotopic areas, plus Brodmann areal boundaries  1.20 Sterotaxic coordinates

·         Select Scene 9 for a view of the flat, inflated, and  average fiducial surfaces (Fig. 1.15). 

·         Click on a few nodes at various locations and note that the Identify Window reports the 3D coordinates for the flat, inflated, and average fiducial surfaces. 

The average fiducial coordinates correspond to coordinates in the ‘711-2B’ stereotaxic space.

Coordinates are reported along with the surface shape values because ‘C’ (coordinates) has been highlighted in the Identify Window.

1.20.1 Latitude-longitude (LatLon) files

·         Text Box: Fig. 1.15. Scene 9. Flat,  inflated, and average fiducial maps.Press Toolbar: Spec.

·         Press Specification File: Misc: Latitude-Longitude Files: Open to load the PALS_B12.LR.latlon file.  Press Replace, then OK to the Choose Columns to Load popup.

·         Now click on a few nodes and note that the Identify Window also reports the latitude and longitude value for each highlighted node.

This requires that the ‘L’ (latitude-longitude) button be selected in the Identify Window.

·        Press Toolbar: Spec, then de-select Auto Close

1.20.2 Latitude-Longitude isocontours.

·         Press Specification File: Borders.

·         Open the LAT_LONG_Rainbow.bordercolor file and press Replace.

·         Open the Human.PALS_B12.LR.LAT-LONG.73730.borderproj file, press Replace.  

·         Close the spec file window.

·         Latitude and longitude isocontours are shown on flat map (main window) and inflated surface (Window 2), and the average fiducial surface (Window 3)  

·         Select Page Selection: Border: Main, then press Display Color Key.

·         Press the color bars next to various latitude and longitude isocontours to highlight their location on the surface.

·         Click on a node near one of the latitude-longitude borders and note that the Identify Window reports on the border identity as well as the node values.

·         (Optional) Save the scene as: Flat, Inflated, Fiducial (Latitude-longitude; IDnode = 3D variability)  PALS-B12 Right.

1.21 Areal estimation files (fuzzy transitions)

The boundaries delimited by contours in border files and sharp transitions between painted areas belie the inherent uncertainties in identifying areal boundaries in any one individual plus the variability across individuals.   One way to represent spatial uncertainty is with ‘areal estimation’ files, in which the transition between one area and another is graded over a specified spatial extent.

·         Press Toolbar: Spec and de-select Auto Close.

·         Select  Spec File: Paint, then open Areal Estimation Files – Human.PALS_B12.LR.COMPOSITE.73730.areal_estimation, then press Replace.

·         Press Spec: Borders: Human.Cerebral.Composite.bordercolor and press Replace.

·         Open Border Projection: PALS_B12.LR.BOTH.COMPOSITE_AREAS... and press Replace.

·        Close the spec file window

·        Select Page Selection: Borders: Color: All Off, then toggle Brodmann back On.

·        Press Border Color Key: Update.

·         Select Page Selection: Overlay/Underlay-surface, then press Primary Overlay: Areal Estimation and select Brodmann from the Areal Estimation pulldown menu to see a fuzzy map of Brodmann areas underlying the Brodmann areal boundaries.

·         Toggle Identify Window: A On (gray) and Identify Window: B Off (white).

·         Click on a node near a ‘T-junction’ where several areas and note that the Identify Window reports fractional estimates for three or four Brodmann areas that are in the vicinity of the selected node

These estimates are NOT true probabilities in any statistically justified sense, so they should be interpreted with caution!

·         Select Page Selection: Areal Estimation, then select Visuotopic for a graded-transition map of visuotopic areas.

·         Select Modalities - RIGHT for a graded-transition map of functional modalities for the right hemisphere (Fig. 1.16B). 

1.22 Metric files (surface & volume)

1.22.1 Probabilistic architectonic areas

·         Select Page Selection: Scene, then select Scene 10 to view a map of Brodmann areal boundaries on flat and inflated surfaces, plus a coronal slice of the average MRI volume. The Brodmann borders are colored using the area colors.

·         Press Toolbar: Spec then Spec File: Volume.

·         Open Volume Files – Functional: Human.ZILLES_ProbabilisticArchitectonic_COMPOSITE… and press Append

·         Select Page Selection: Overlay/Underlay – Volume.

 

Text Box: Figure 1.16B. Functional modalilties estimation map plus Brodmann areal boundaries.Text Box: Figure 1.16A. Broadmann areal estimation map plus areal boundaries.               

·         Press the Primary Overlay Functional-View button and select Brodmann_44 from the Functional-View pulldown menu to view a probabilistic map of area 44 from the Zilles lab (Amunts et al. 2004) in the volume slice.

This volumetric probabilistic map was obtained by volume-based registration from individual postmortem subjects to MNI stereotaxic space using a linear transformation, then an affine  transformation from MNI space to the 711-2B space in which the PALS atlas was generated. 

·         Press Toolbar: Spec then Spec File: Metric.

·         Open Metric Human.ZILLES.RIGHT. ProbabilisticArchitectonic_18-Areas…

·         Press the OK button to load all 18 columns of this metric file.

·         Select Page Selection: Overlay/Underlay – Surface, press the Secondary Overlay: Metric button, and select Brodmann_1 from the Metric pulldown menu  to view a probabilistic map of area 1 from the study of Geyer et al. (2001) on the flat map and inflated surface. 

·         Select Page Selection: Metric: Selection tab, then press the View: Brodmann_44 button (#8) to see probabilistic area 44 after mapping from the volume onto the PALS surface (Fig. 1.17).

In terms of file format, metric files and surface shape files are identical. Categorizing them differently is nonetheless useful because they typically contain different types of data that are useful to combine in an overlay/underlay arrangement.

·         Text Box: Fig. 1.17. Probabilistic area 44 (Amunts et al., 2004).Select Viewing Window 3: All from the pulldown volume slice selector (current setting: C(XZ).

·         Click on a few nodes within probabilistic area 44 on the PALS surface in the main window and note how the volume slices move to corresponding points.

Note that probabilistic area 44 of Amunts et al (2004 – referenced in the query button) is centered well within Brodmann’s area 44 boundaries.  This concordance is especially noteworthy given the numerous methodological differences in how the two data sets were mapped to the PALS atlas.

The values reported in the Identify window are more closely related to underlying probabilities than with the areal estimation maps of the preceding section.  However, they are not in any sense true probabilities

·         Select Metric: Brodmann_45 (#9) to see a probabilistic map of area 45.

·         Select Page Selection: Overlay/Underlay – Volume.

·         Select Brodmann_45 from the Functional-View pulldown menu to view a probabilistic map of area 45 from the same study (Amunts et al. 2004) in the volume slice.

·         Click on a few nodes within probabilistic area 45 on the PALS surface and note the concordance between surface and volume maps of area 45.

·         Select Page Selection: Metric, then press the Settings tab. 

·         Select Threshold Type: Average Area to see a more restricted map of the extent of area 45, matched to the average surface area of probabilistic area 45 mapped to each of the 12 contributing subjects.

·         Select Threshold: Show Subthreshold Regions in Green to see the probabilistic area 45 map expanded to its original extent, but with the subthreshold region shaded light green.

This and other probabilistic architectonic maps in this dataset represent the result of two distinct probabilistic mapping operations:  (i) volume-based registration from individual postmortem subjects to stereotaxic space, and (ii) multifiducial mapping of the probabilistic volume onto the PALS atlas surface.  The subthreshold regions represent locations where there is a lower but still finite probability of area 45 being present in any given individual.

1.22.2 Viewing fMRI data – Functional Volume and metric files.

Most fMRI studies are analyzed by volume registration of individual subjects to a standard stereotaxic atlas, then carrying out statistical analyses on the registered volume data. The PALS atlas can be used to view volume-averaged fMRI results on a surface without the biases imposed by any individual subject’s particular convolutions.

§         Select  Scene 11 to view the PALS average volume (main window), plus the inflated and flat surfaces (windows 2 and 3), ready for loading of fMRI data.

·         Press Toolbar: Spec then Spec File: Volume.

·         De-select Auto Close, then Open Volume Files – Functional: Burton_04_VibroTactile_EARLY_BLIND… and press Replace

·         Open Volume Files – Functional: Burton_04_VibroTactile_SIGHTED and press Append

·         Close the spec dialog

·         Select Page Selection: Overlay/Underlay – Volume.

·         Press the Primary Overlay Functional-View button for a view of fMRI activations in a vibrotactile task in early blind subjects (Burton et al., 2004) (Fig. 1.18A). 

§         Select Page Selection: Metric and press the Settings tab.

              Note that the metric settings are available for controlling functional volume displays even though there is no currently loaded metric file.

§         Press Display Mode: Negative to see just the negative activations, then Display Mode: Positive to see just the positive activations.

To compare similarities and differences for these and other tasks across the entire hemisphere, it is advantageous to view the fMRI data mapped to the PALS atlas surface.

§         Press Toolbar: Spec then Spec File: Metric, open the PALS_TUTORIAL.RIGHT.COMPOSITE.73730.metric file

§         Select Erase All Existing Columns and press the OK button.

§         Select Page Selection: Overlay/Underlay - Surface and press the Secondary Underlay: Metric button.

§         Select the first entry in the Metric pulldown menu (AFM_BURTON_04_Vibrotactile_EARLY_BLIND).

§         Select Page Selection: Metric and select Palette: fidl from the pulldown menu.

§         Press the Display Color Bar button.

§         Press the Selection tab and toggle between the AFM (Average Fiducial) and the MFM (Multi-fiducial) maps of Burton_04_VibroTactile_EARLY_BLIND (Fig. 1.18A, B).

In AFM, each node is assigned the value of the voxel in which it resides (or an interpolated value, depending on the specific algorithm chosen).  In MFM, each node takes the average value after mapping the volume to each of the 12 contributing hemispheres.  MFM gives a smoother map and the best estimate of spatial localization; AFM gives the most likely peak value.

·         Text Box: Figure 1.18B. Average fiducial mapping (AFM) vs multi-fiducial mapping (MFM) of vibrotactile activations in early blind subjects on inflated and flat maps.Text Box: Figure 1.18A. Volume-averaged fMRI in early blind subjects doing vibrotactile tasksPress the MFM_BURTON_04_VibroTactile_SIGHTED button

·         Select Page Selection: Overlay/Underlay – Volume.

§         Select Functional-View: Burton_04_VibroTactile_SIGHTED from the pulldown menu for a view of fMRI activations in a vibrotactile task in normally sighted subjects (Burton et al., 2004).

The activation pattern is very different in subjects blind since birth compared to the sighted controls but it is difficult to appreciate the overall pattern of differences in the volume slices.

§         Select Page Selection Metric  and press the Metric: Selection tab, and select MFM–BURTON_04_VibroTactile_SIGHTED to view the activation pattern from the same Vibro-tactile task, but in normally sighted subjects (Fig. 1.19 left vs right panels).

Note the dramatic difference in extent of activations in the two groups, particularly in occipital cortex.

§         Press the Metric: Settings tab, then the Threshold: Threshold Type: User from the pulldown menu to see the same map without thresholding.

§         Select the Threshold: Threshold Type: Average Area option (Fig. 1.18B).

§         Press Threshold: Show Subthresh Regions in Green to view the maximal extent of the MFM positive activations.  In essence, this shows the estimated maximal spatial extent of significant activations that might be encountered in any individual in a population.

§         Toggle Show Subthresh Regions in Green off.

 

Text Box: Figure 1.19. Comparison of activations in sighted (left) vs. early blind (right) subjects.

1.22.3 Viewing fMRI activations in relation to other experimental data.

§         Select Scene 12: fMRI Vibrotactile. . .

§         Select the Display Control: Page Selection: Border page, and press the Main tab.

§         Text Box: Figure 1.20. Early blind vibrotactile activaations relative to visuotopic areasToggle Show borders on.  Many different borders should appear.

§         Press the Border: Color tab, then the All Off button.

§         Select the Visuotopic button to see just the borders of visuotopic areas (Fig. 1.20).

In early blind subjects, there is activation of the entire swath of visuotopic areas (especially in dorsal regions), plus an extended additional domain, especially in posterior parietal cortex. 

§         Press Border: Main Tab: Display Color  Key, then press Override Border Colors with Area Colors.

§         Return to the Page Selection: Metric page Selection tab and select the MFM BURTON_04_VibroTactile_SIGHTED column to see that there is very little activation of visual cortex in normally sighted subjects.

§         Press the Border Color Bars to highlight specific areas of interest and the border name to see their identity.

§         Return to the Page Selection: Metric page and select the AFM - DENYS_EtAl_JN04_OBJECT-Related_LOC_SPM99 column to see the activation of visual cortex from a study on object-specific activations (Fig. 1.21A).

Text Box: Figure 1.21B.  Object-specific activations by multi-fiducial mapping (MFM) from Denys et al. (2004). Subthreshold regions are shown in green.Text Box: Figure 1.21A. Object-specific activations mapped by average fiducial mapping (AFM) from Denys et al (2004).If nothing happens, make sure the ‘Apply Metric L-toL, R-to-R...’ button is deselected.

§         Press the query (?) button to see more information about this study, including the link to the online publication (Denys et al., Select the MFM - DENYS_EtAl_JN04_OBJECT-Related_LOC_SPM99 column to see the difference between MFM (multi-fiducial mapping) and AFM (average fiducial mapping) when mapping the SPM99 volume data onto the PALS atlas surface.

§         Press the Metric: Settings tab.

The Threshold Type (lower right) is set on Average Area, which is set at a value of 2.05 for positive values.  This value is computed automatically in the multifiducial mapping process (see Van Essen, 2005a).

§         Press the Show Subthresh Region Green button to see the larger expanse of subthreshold regions (Fig. 1.21B).  These in effect show the maximal extent of activation taking individual variability into account (Van Essen 2005).

See User’s Guide (pp. 19-22) for instructions on using Surface: ROI operations to analyze regions of interest (e.g. from activation patterns in metric files).

1.22.4. Mapping fMRI data

Visualization of fMRI activation patterns on the PALS atlas from different paradigms, projects, and publications can be a powerful strategy for objective comparisons across neuroimaging studies.  To make this process efficient and effective, several components need to come together.

1)      Mapping fRMI activations onto the PALS atlas as a rule and routine, rather than occasionally or as an exception.

2)      Providing adequate annotation (metadata) so that the data can be properly evaluated.

3)      Submitting the data to SumsDB.

Section 5.1 provides guidance on how to do each of these steps

Part 2 shows how to make use of the fMRI data already in SumsDB.

1.23 Foci and Foci projection files; Stereotaxic Neuroimaging Foci

Many types of spatial neuroimaging data are reported in terms of the stereotaxic coordinates of functional or structural data.  Caret can handle such data as ‘foci’ files (in which the data are stored by the x,y,z coordinates in a specific stereotaxic space such as 711-2B or SPM99) or as ‘foci projection’ files (in which the data have been projected to the atlas surface).  The process for entering additional foci is now relatively streamlined (Section 5.2)

Note that the foci appear only in the work window, where the fiducial surface is viewed. The foci are viewed in relation to the PALS average fiducial surface in 711-2B stereotaxic space, but the foci derive from studies in five  different spaces (SPM96, SPM99; FLIRT, MRITOTAL, T88.)

The remaining foci in the left hemisphere will appear, without an underlying surface.

1.23.1 Foci Color Key

1.23.2 Projecting foci

Over the next minute of so, all of the loaded foci will be projected to the atlas surface and will progressively become visible in the other windows (inflated and flat surfaces). In the projection process, each focus is mapped not to the Average fiducial surface loaded in the main window. Instead, each focus is mapped to the particular average fiducial surface registered to the same stereotaxic space as the data were originally reported. One the projection process is complete, most of the foci in the main window will jump to slightly different locations, indicating that they are now all in a common space (FLIRT).

1.23.3 Selective visualization of foci and metadata

This report includes the coordinates of the focus as originally reported by Rushworth et al. (2001) as [“Original Stereotaxic Position (MRI Total): 50, -35, 30] and in addition shows the coordinates of the same focus in FLIRT space: 49, -36, 29. The focus here (RushworthEtAL_Response Switch) indicates that this was a significant activation in a behavioral responses-switching task.

·         If no focus information is reported in the Identify Window, zoom in on the Window 3 flat map, then click again on the focus.

In this instance, the link goes directly to Table 1 of the study (“Parietal cortex activations identified in each task comparison”).  The highlighted focus is at the bottom of the RS (‘response switch’) column. Clicking on ‘Return to Article’ in the upper right brings up the section of the Results describing this table.  Most of the other foci are in posterior parietal cortex.

·         Click on a focus in the parietal cortex on the flat map to obtain focus-specific and study-specific information from this study, which reports activations with optic flow and heading estimation.

In this study, the activation foci were reported in SPM96 stereotaxic coordinates. 

                                In this case the link goes to the beginning of the Peuskens online article. (Including Table-specific links as with the preceding example involves more tedious data entry, but has obvious advantages.)

 

1.23.4 Reporting coordinates in multiple stereotaxic spaces

The focus has SPM96 coordinates of (6, 0, 70) but T88 coordinates of (3, -1, 63), (i.e. 7 mm different in the z axis). 

The coordinates for different spaces often differ by 5 - 10 mm along one or more axes.

1.23.5 Selective viewing by foci color and class

In this case, there is only one class per study (color), but in general this need not be the case, so having the option to select by foci class as well as color adds useful flexibility.

·            Press Foci: Class: All on

·            Press Toolbar: Spec: Foci and deselect the autoclose button.

·            Open JNeurosci 2000 focicolor and press the Append button.

·            Open: Foci: Human.PALS-B12.LR.JN00_STEREOTAXIC.fociproj and press the Append button to see about twice as many foci available for analysis.

1.23.6 Viewing bilateral vs. unilateral foci

·            Press Foci: Main, then toggle Show Foci in Correct Hemisphere Only off to see left hemisphere foci combined with right hemisphere foci.

The alternative of viewing both hemispheres concurrently with foci projected in a hemisphere-specific way, has obvious advantages and is illustrated below (Section 1.32.3).

·             Toggle Show Foci in Correct Hemisphere Only back on again

1.23.7 Selective deletion and regrouping of foci

Foci extracted from published neuroimaging studies may initially be read into Caret in a different grouping than are desired for subsequent analyses. Caret allows for convenient regrouping of files, especially when they reflect categories encoded by foci class and foci color entries.

·         Press Foci: Class: All Off, then select the six classes that deal with memory (Working-memory, Working-memory_set shifting, Memory-visual discrimination, Memory-Encoding, Lesion-working-memory_Conditioning, Face-Recognition_Memory_Encoding).

·         Select Layers: Foci: Delete Foci Not Displayed in Main Window Surface and press yes in the ‘Are you sure’ popup.

The Foci:Class list is now streamlined to show only the displayed foci classes for the right hemisphere

Note: If you want to save foci from both hemispheres meeting the other criteria, be sure that Show Foci in Correct Hemisphere Only is toggled Off.

·         Save (S) the foci projection file as JN00-01_Memory.RIGHT.77730.fociproj.

·         Press the Foci: Colors tab.

·         Select Layers: Foci: Delete Foci Colors Not Matching Foci and press yes in the ‘Are you sure’ popup.

The Foci: Color page is now streamlined to match only the displayed subset.

·         Save (S) the foci color file as JN00-01_Memory.focicolor

·         Press Toolbar: Spec: Foci

You have now generated a compact dataset that cuts across multiple years and groups foci according to function.  This approach can be used more generally to efficiently generate datasets that are grouped by a variety of criteria.

1.24.8 Exporting Foci to spreadsheets

·         In the Main Window, select Model: FIDUCIAL Human. . . FLIRT...

·         Select File: Save Data File: Foci file, and save the foci file as JN00-01_Memory.RIGHT.FLIRT.foci.

This will save the file in the default XML format

·         Select File: Save Data File: Foci File

·         Select Data File Encoding: Comma Separated Value File

·         De-select Add File Name Extension. . .

·         Save the file as JN00-01_Memori.RIGHT.FLIRT.foci.csv

This file can be read by Excel and other spreadsheet programs. 

1.24 Viewing & editing text files

·         Select Window: Text File Editor to bring up a text editor that has many general-purpose characteristics plus some Caret-specific features

·         Press Text File Editor: Open. The default listing shows all files in the current directory.

·         Press Files of Type: Foci File and open the JN00-01_Memory.FLIRT.foci file.

The file is in XML format, which is gibberish to many, but has important technical advantages

·         Select Window: Text File Editor.

·         In this second text file editor press Open, then select Files of Type: Comma Separate Value File (*.csv)

The csv version of this file is much more compact than the XML version in the other text editor, and it can be read directly by spreadsheet applications.

These coordinates are now all represented in FLIRT space, irrespective of the space in which they were originally represented.

1.25 Standard scenes for ongoing analyses.

This section introduces a standardized set of scenes and associated data sets intended to facilitate use of PALS as a workhorse data set for a wide variety of ongoing analyses.

§         Select File: Open Spec File (or, press -N).

§         Select the PALS_B12.RIGHT.STANDARD_SCENES.73730.spec file.

§         Press the Load Scene(s) button.

§         Press the New Spec Only button in response to the popup query about whether to load two spec files concurrently or to just load the new one.

The scene file contains 13 scenes, each intended to be a useful launching point for a variety of visualization and analysis purposes.  Most are very similar to the pre-packaged ones used in the preceding section, but with scene names slightly modified.

§         Select the first scene: Inflated surface (Avg depth, orange-yellow) [flat, very-infl loaded].  This is the same as scene 1 of the tutorial, but with additional coordinate files loaded, plus the PALS latitude-longitude file.

§         Press Scenes: Check all Scenes, then press Continue in the first popup; window and 5 seconds in the second window to initiate a sequences in which you can view each scene successively to get a feel for its potential utility in ongoing analyses.

As will be more apparent in the next section, the left and right hemispheres are not completely mirror-symmetric, and these asymmetries are explicitly represented in the coordinate and surface shape files for the two hemispheres.

1.26 Customizing your own PALS scenes and spec files

You may find that many of the currently loaded scenes are useful but that others are not for your ongoing project-specific needs.  Caret allows you to customize a spec file and an associated scene file in an efficient way, and then to transfer just the desired files to a target directory for launching a new set of analyses.

·         Highlight the first three scenes in the scene file.

·         Press the ‘Create spec from selected scenes’

·         Enter ‘PALS-B12.TEST.73730.spec’ for the spec file and ‘TEST-scenes.scene‘ (the entry must end in ‘scene’ to be valid) for the scene file, then press OK

This will generate a new spec file that lists just those files needed to generate the selected scenes.

·         Select Open Spec file (N): ‘PALS-B12.TEST.73730.spec’

·        Press Load Scene(s) and open the first scene.

·         In a terminal window, go to the CARET_TUTORIAL_Sept06/ directory

·         Enter mkdir TEMP

·         In Caret, Select File: Copy Spec File.

·         Select Copy This Spec File: PALS-B12.TEST.73730.spec

·         Select Into This Directory: TEMP

·         Press the Copy Data Files button, then press Apply.  After a few seconds a popup window will indicate success.

When you start on a new project that involves the PALS atlas, you may find it useful to create and copy appropriately customized scenes and spec files to the relevant project-specific or case-specific directory.

                Note: When changing from one scene to the next, be aware that some file types (e.g., coord, topo, paint, metric) are kept loaded in memory even if they were not part of the newly selected scene. This can be handy sometimes and inconvenient at other times. Use Unload All Files Except Scene if you want to bypass this feature.

1.27 Uploading data to SumsDB

Uploading data sets to SumsDB can be done very easily at the end of a working session.

·         In the Menu bar, select Comm: connect to SumsDB Database

·         Select Database Login: Username: caret_tutorial, password ‘pals_rules’, then press Next

·         Press Database User Information: Next

·         Press Database Mode: Upload Files, then press Next

·         Press Upload Files: Add Files

·         Select File Name: PALS_B12.TEST.73730.spec and press Open

·         Do NOT press Finish, as this will take time, and an equivalent data set is already in SumsDB.  Note that only new files or files that have been altered will be added to the database archives.

The data set you were about to upload is in fact already in SumsDB and will be used for viewing and downloading in the next section.

1.28 Viewing multiple spec files concurrently

The files currently loaded in Caret are based on ‘standard-mesh’ surfaces that contain 73,730 nodes. Many other data sets of interest (e.g. surface reconstructions from individual hemispheres) contain a different number of nodes and therefore cannot be concurrently loaded as individual files.  However, Caret does allow concurrent loading of multiple independent spec files whose data files can be viewed in alternation.

·         Press Scene: Unload All Files Except Scene and press yes.

·         Open the first scene.

·         Select Open Spec File; select the  INDIVIDUAL/directory and open: Human.Subject 1_Orban04.RIGHT.148958.spec

·         Press Load Scenes

·         Press the Keep Loaded Spec button

This shows data from individual subject initially process using FreeSurfer, then converted to Caret format (see Section 2.18.1 and Caret User’s Guide, p. 13).

·         Text Box: Fig. 1.24.  Fiducial and inflated surfaces of an individual subject in a data set concurrently loaded with the PALS atlas data.Open the first scene (fMRI...) to see fMRI data (objects vs. scrambled objects activation) on fiducial and inflated surfaces of Subject 1 from Denys et al. (2004) as in Fig. 1.24.

The FreeSurfer fiducial surfaces are based on the gray-white boundary and thus differ in appearance from SureFit-generated representations of the cortical midthickness (layer 4).

·         Select Model and note that five coordinate files are currently loaded.  The R-prefix indicates that these are all right hemisphere data (based on the spec file ‘structure’ entry), three from the subject 1 data set and two from the PALS atlas.

·         Select the PALS_INFLATED surface and note that all windows switch back to the PALS scene and data set.

·         Select the Subject_1 INFLATED surface and note that the scene listing returns to the subject 1 scenes.

1.29 PALS left hemisphere analysis data set.

The surfaces up to this have been entirely from the PALS right hemisphere Naturally, there are many data sets that need to be analyzed for the left hemisphere or for both hemispheres concurrently. 

§         Select File: Open Spec File (-N).

§         Select the PALS_B12.LEFT.STANDARD-SCENES.73730.spec file.

§         Press the Load Scene(s) button.

§         Press the New Spec button.

·         Select the first scene: PALS LEFT inflated surface (Avg depth, orange-yellow) [flat, very-infl loaded].  This is the same as the first scene of the preceding spec file, except that it is for the PALS left hemisphere instead of the right.

Just as with the preceding right hemisphere scene file, there are 12 scenes, each intended to be a useful launching point for a variety of visualization and analysis purposes.

§         Press Scenes: Check all Scenes, then press Continue in the first popup; window and 5 seconds in the second window to initiate a sequences in which you can view each scene successively to get a feel for its potential utility in ongoing analyses.

As will be more apparent in the next section, the left and right hemispheres are not completely mirror-symmetric, and these asymmetries are explicitly represented in the coordinate and surface shape files for the two hemispheres.

1.30 Concurrent viewing of left and right hemispheres.

Concurrent viewing of left and right PALS hemispheres is useful for many purposes and is facilitated by Caret options that faithfully display left-on-left and right-on-right data without inordinate effort.

§         Select File: Open Spec File (-N). and select the PALS_B12.BOTH-HEMS.DEMO.73730.spec file.

§         Press the Load Scene(s) button, then press the New Spec button.

§         Select the FLAT, STANDARD Contrast… scene for simultaneous views of the left and right hemisphere flat maps with the standard grayscale contrast (Fig. 1.25)

§         Select Scene 2 VeryINFLATED, Orange-yellow Contrast… to see the gold-shaded depth maps on each hemisphere.

Text Box: Figure 1.25.  Left and right PALS flat maps, with averge sulcal depth maps shown separately on each hemisphereThe asymmetries between left and right hemisphere depth maps are most prominent in lateral temporal cortex.  The STS is deeper (darker) in the right hemisphere, and the average sulcal depth maps appear quite different in the vicinity of the dorsal STS (highlighted node in Fig. 1.26), as discussed further below. 

1.31 Automatic hemisphere-specific data displays.

The hemisphere-specific assignment of sulcal depth maps is handled using options in the Surface Shape page.

·         Text Box: Fig. 1.26. Corresponding nodes in the left and right parieto-temporal cortex, where average sulcal depth maps differ markedly.Select Page Selection: Surface Shape: Selection.

·         Toggle Apply L-toL, R-to-R Matching to Coord Files off.

·         Select the AVERAGE B1-12 LEFT DEPTHnr sulcal depth column (#5). 

The right hemisphere surface will now display average sulcal depth for the left hemisphere instead of the right.  The left hemisphere surface will remain unchanged.

·         Select the AVERAGE B1-12 RIGHT DEPTHnr sulcal depth column (#1). 

Both left and right surfaces will now display the right hemisphere depth map.

·         Switch between the left and right DEPTHnr columns again if needed to see the changes on both maps.

·         Toggle Apply L-toL, R-to-R Matching to Coord Files back on.

·         Select the AVERAGE B1-12 RIGHT DEPTHnr sulcal depth column (#5). 

The highlighted button will automatically change back to the LEFT depth map, obeying the constraints of L-to-L and R-to-R mapping.  However, this occurs ONLY if the column headers for left and right are matched except for RIGHT vs LEFT in the text string.

·         Place the cursor over the Apply L-toL, R-to-R Matching to Coord Files text and wait a moment.

A popup window will explain how this option works, in case you want a quick reminder in the future.

1.32 Individual Surface-specific data displays.

Caret also allows independent control of what is displayed on each surface configuration, regardless of column name and whether the surfaces are from the same or opposite hemispheres.

·         From the pulldown Surface Coloration Applies To Menu (current listing: All Surfaces), select the VERY INFLATED: Human.PALS_B12.LEFT…. coordinate file.

·         Toggle Apply L-toL, R-to-R Matching to Coord Files off.

·         Select the 3D VARIABILITY - LEFT_HEM Human.PALS_B12 sulcal depth column (#7). 

This will change the display on the left hemisphere surface but leave the right hemisphere unchanged.  The 3D variability map represents the previously illustrated (Fig. 1.9) variability in 3D node position, which can also be displayed using the appropriate selection in the Node ID Deviation in Surface Shape: Settings.

·         Select the DEPTH VARIABILITY - B1-12 LEFT (DEPTHnr) sulcal depth column (#8). 

This will again change the display on the left hemisphere surface but leave the right hemisphere unchanged.  The depth variability represents the standard deviation of the individual sulcal depth values at each node (cf. Fig. 1.8).

·         Select the Surface Coloration Applies To: VERY INFLATED: Human.PALS_B12.RIGHT…. coordinate file.

·         Select the Low Contrast AVERAGE B1-12 RIGHT DEPTHnr sulcal depth column. 

In this way, unrelated types of data can be displayed on different surface configurations in different windows, using up to the maximum of 10 windows. 

TIP: If you want to display different data on the same configuration (e.g., the right hemisphere flat map), this can be done by saving the coordinate file of interest with a slightly different name (e.g., <filename>.copy2.coord), and loading multiple versions/names of the file concurrently.

1.32.1 Left-Right Asymmetries

§         Select Page Selection: Scene  and select Scene 3 (Average FIDUCIAL (FLIRT)) to see the left and right average fiducial surfaces.

Text Box: Fig. 1.27 Corresponding STG nodes in the left and right hemisphere average fiducial surfaces (FLIRT space).These were generated from hemispheres registered to the MNI-152 population-average target using the FLIRT registration algorithm (http://www.fmrib.ox.ac.uk/fsl/flirt/).  In general, we consider the FLIRT-registered average fiducial surfaces (Fig. 1.22B) to be a suitable ‘preferred choice’, because the target atlas represents the actual average shape of a large population of normal subjects, and the registration involves linear transformation rather than nonlinear methods that can introduce significant local distortions .

·         Click on a node on the superior temporal gyrus (STG) of the right hemisphere, as in Fig. 1.27.

Note that a corresponding node is highlighted in the left hemisphere. The STG is wider on the right, and as previously noted the neighboring STS is deeper on the right.  There are many other differences in detail between the left and right average fiducial surfaces, but determining which of these are significantly different requires explicit testing (see below).

The Identify Window reports the coordinates for both left and right inflated surfaces. Only single latitude and longitude value is reported; this applies equally to both hemispheres.

·         Select Scene 4: INFLATED, Orange-Yellow contrast.

Note that the STS appears darker (deeper) in the right hemisphere.

The next four scenes illustrate quantitative analyses of left-right asymmetries in sulcal depth.

·         Select Scene 5: DEPTH DIFFERENCE (Cases B1-24) on INFLATED (PALS-B12, Lateral, medial) scene (Fig. 1.28A) to see a map of differences in average depth between left and right hemispheres for Cases B1-24 (Van Essen, 2005a).  The depth difference scale ranges from -12 mm (blue, left deeper) to +12 (red, right deeper).

·         Select Files: View Current Files and scroll down to the Surface Shape File entry. Two files are loaded concurrently in this scene, the second of which (Human....B1-24...COMPOSITE) contains information about left-right asymmetries in a group of 24 normal subjects (Van Essen, 2005a).

·         Select Scene 6: T-map LEFT-RIGHT Asymmetry (Cases B1-24) on INFLATED (PALS-B12, Lateral, medial) scene (Fig. 1.28B). 

The t-maps (paired t-test, in which a paired t-statistic was computed at each node using the 24 individual depth values for each hemisphere) are thresholded at |t|>2; the range extends over +/-8.

Text Box: Fig. 1.28A.  Depth difference map for left-right 	Fig. 1.28B. T-statistic map of left-right asymmetry
average sulcal depth (cases 1-24)   

·         Select Scene 7: LEFT-RIGHT Asymmetries on INFLATED RIGHT (Lateral, medial) Paired t-test (|t|>2) (Fig. 1.29A) to see the five statistically significant left-right asymmetries in sulcal depth.

Statistically significant differences were identified using a permutation analysis of clusters having |t| > 2.  Even more asymmetries are revealed using a larger sample of 72 normal subjects (Van Essen, 2005b).

Text Box: Fig. 1.29A. Lateral and medial views of			Fig. 1.29B. Left-right asymmetries on very
 left-right asymmetries in sulcal depth.			inflated surface          

 

·         Select Scene 8:  LEFT-RIGHT Asymmetries on VeryINFLATED… to see the same five statistically significant left-right asymmetries on the very inflated surfaces (Fig. 1.29B).

1.32.2 Viewing probabilistic maps bilaterally

·         Text Box: Fig. 1.30  Bilateral probabilistic map of area 44 in the atlas volume and PALS inflated surfaces.Select Scene 9 to see a map of probabilistic area 44 in the volume (Main Window, 3 slides) and in the inflated left and right hemisphere surfaces (Fig. 1.30).

·         Select Page Display: Metric and note that the ‘Apply L-to-L, R-to-R Matching has been selected.

·         Press MFM Left-Brodman-45 to see the probabilistic area 45 in the inflated surfaces.

·         Select Page Display:Overlay/Underlay Volume, and select Functional View: Brodmann_45 to see a corresponding data set in the in volume.

1.32.3 Viewing surfaces and volumes bilaterally.

·         Text Box: Fig. 1.31  Average MRI volume plus left and right average fiducial surfaces in FLIRT stereotaxic space.Select Scene 10 (Average MRI VOLUME (3-slice) + Average FIDUCIALS (FLIRT) to see the average structural MRI volume for the PALS-B12 individuals registered to FLIRT stereotaxic space, plus the average fiducial surfaces for the two hemispheres (Fig. 1.31).

·         Click on various nodes in the left hemisphere volume in the main window (red surface contours). 

The nearest surface node to the selected voxel will be highlighted in the left hemisphere surface (window 2) and in the corresponding node of the right hemisphere (window 3).

·         Click on various nodes in the right hemisphere volume in the main window (blue surface contours). 

Crosshairs will transiently appear in Windows 2 and 3, but no surface nodes will be highlighted.  This is because the ‘active fiducial surface’ is currently set to be the left hemisphere. You can tell this because the left hemisphere is displayed in the lower left corner of the main window.

·         Press CID in the Identify Window to clear the highlighted nodes.

·         Click on various nodes in the left hemisphere surface (Window 2). 

The corresponding node of the right hemisphere (window 3) will be highlighted, and the cursor will jump to the corresponding voxel in the left hemisphere in the main window.

·         Click on various nodes in the right hemisphere surface (Window 3). 

The corresponding node of the left hemisphere (window 2) will be highlighted, and the cursor will jump to the corresponding voxel in the left hemisphere in the main window, reflecting the current active fiducial surface.

§         Select Page Selection: Surface Miscellaneous   and select the Active Fiducial: Human.PALS_B12.RIGHT….

The surface displayed in the lower left of the main window will switch to the right hemisphere.

§          Click on various nodes in the right hemisphere surface (Window 3)

The cursor will consistently jump to the corresponding voxel in the right hemisphere in the main window, reflecting the switch in the active fiducial surface.

·         Select Scene 11: Avg MRI + ID-sulci; Average FIDUCIAL (711-2C) to see the probabilistic volume of identified sulci, along with the PALS average fiducial surfaces.

In this scene, the volumes and surfaces are in 711-2C space (rather than FLIRT) because this is the space in which the probabilistic volume of identified sulci was generated.

·         Select Scene 12: Avg MRI + ID-sulci; INFLATED to see the probabilistic volume of identified sulci, along with the PALS inflated surfaces (Fig. 1.32).

1.32.3 Viewing neuroimaging foci bilaterally

·         Press Display Control: Unload All Files Except Scenes, then press Yes.

·         Select Scene 13: JNeuroscience (2000, 2001) foci on PALS_B12FLAT,LEFT,RIGHT (6 Avg Fiducial) .

·         Text Box: Fig. 1.32.  Probabilistic sulci in volume slices plus PALS inflated left and right hemispheres.Click on a focus and note that its stereotaxic coordinate are reported in eight different spaces for either the left or the right hemisphere.

·         Select Page Selection: Foci  and toggle the Show Foci on Correct Hemisphere only off to see all 600 foci mapped in duplicate onto each flat map (Fig. 1.33).  

All of the other options described in Section 1.24 (Foci and Projection Files) can be used here, including selective viewing of foci by name and/or class and creation of smaller files containing only the selected subset.

1.32.4 Standard –scenes for bilateral viewing

§         Text Box: Fig. 1.33  Stereotaxic activation foci mapped bilaterally onto PALS flat maps.Open a new spec file: PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec

§         Load the scene file.

§         Select Check All Scenes and choose a spec interval.

§         View the 15 scenes in succession, and keep in mind which ones you may find useful in the future.

132.5 Scenes for stereotaxic foci analysis

§         Open a new spec file: PALS_B12.BOTH-HEMS-For-STEROTAXIC-FOCI-ANALYSES.73730.spec

This is a spec file customized for stereotaxic foci analyses because it contains fiducial surfaces for eight commonly used stereotaxic spaces.

·         Select the Avg Fiducial (FLIRT, Both Hems) for stereotaxic foci analyses scene.

This is a useful starting scene when generating foci files de novo, using the Map Stereotaxic Focus option (see the Caret User’s Manual Section 1.4.3, Caret Analysis Steps).

·         Select the FLAT (Both hems) plus loaded Avg Fiducials (FLIRT) scene.

·         Press the Model pulldown menu in the main window and note that there is only one pair (left-right FLIRT) of FIDUCIAL files loaded (plus 3 other configuration left-right pairs). 

This is a useful starting scene when loading and viewing existing foci projection files if you DO NOT want separate reports of coordinate values in multiple stereotaxic spaces.

·         Select the FLAT (Both Hems) plus loaded Avg Fiducials (8 pairs) for foci reports) scene.

·         Press the Model pulldown menu in the main window and note that there are eight left-right pairs of FIDUCIAL files loaded.

This is a useful starting scene when loading and viewing existing foci projection files if you DO want separate reports of coordinate values in multiple stereotaxic spaces.

 

-- End of Part 1


Part 2. SumsDB and WebCaret.

2.1 Overview

SumsDB (the Surface Management System DataBase) provides convenient access to a growing body of neuroimaging and related data. It contains:

SumsDB provides multiple levels of data access and security:

Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret

WebCaret provides online ‘Caret-style’ visualization while circumventing software and data downloads. It is a ‘server-side’ application running on a linux cluster at Washington University.

- Links from figures in online journal article to corresponding scenes in WebCaret

- Links from metadata in WebCaret directly to relevant online publications and figures

Searching and data-mining with SumsDB and WebCaret is flexible and powerful:

·         Spatially based queries

- proximity to stereotaxic coordinates

- overlap with selected fMRI activations (metric files)

- overlap with identified cortical areas (paint files)

-          currently loaded datasets

-          ‘processed’ datasets

-          all public SumsDB data

-          restricted access data

                  -     viewed in WebCaret

                  -     combined with other loaded data sets

                  -     downloaded directly

Part 2 is organized as follows:

                  -     Overview of SumsDB home page

                  -     WebCaret scene visualization and navigation

                  -     Navigating archives, spec files, and data files in SumsDB

                  -     Searching and data mining

                  -     Uploading data

All but the uploading can be done without a SumsDB account or logon requirement.

2.2 Getting Started in SumsDB

§         Open a browser window.

§         Go to http://sumsdb.wustl.edu/sums/

The SumsDB home page (Fig. 2.1) provides many options for accessing commonly used data sets (atlases, etc.) as well as entry points for more general navigation and search options.

2.3 SumsDB Menu bar overview.

Text Box: Fig. 2.1.  The SumsDB home page (add arrows, labels)The menu bar provides quick access to many commonly used SumsDB options.

§         Place the cursor over each entry in the Menu bar and note the different subcategories. 

-Directories includes the Inbox, Tutorials (see Section 2.21), Publications (see Sections 2.9 and 2.10), and Atlases (see Section 2.8).

 

·         Place the cursor over Browse/Search and note the 10 options available for browsing and searching.

              -     Basic and Advanced Archive Search allows searching for files that meet a variety of criteria, including filenames, file type, keywords (Section 2.19).

-                  Region of Interest Search (Sections 2.11 – 2.15), Foci Study Search, and Foci Data Search (Section 2.17) are applied to specific data types and to specific data sets that are published and have properly annotated metadata.

              -     Search Results includes various ways to display recent search results.

            -       Help includes sources of information about SumsDB, WebCaret and their usage.

2.3.1 Useful links

The Useful Links (far right column) contains a number of useful resources and sources of information.

·         Click on Useful Links: Online SumsDB tutorial to bring up an online version the same document you are currently using (Part 2 = SumsDB and WebCaret only).

2.4 WebCaret Demo

Text Box: Fig. 2.2 WebCaret Menubar, scene selection, toolbar; scene (PALS inflated surface) The fastest route to launching WebCaret is to click on one of the four multi-panel images near the top of the home page.

·         Click on the Human PALS atlas image  to launch a demo of the PALS atlas.

After a few moments (while the data are loaded onto the WebCaret server – a linux cluster at Wash U), a lateral view of the inflated PALS surface will appear (Fig. 2.2)

The surface data you just selected will take a moment to load (~10 sec - 1 min, depending on file sizes). While you are waiting:

For an overview of WebCaret's surface visualization capabilities, 
click here: Viewing Surfaces with WebCaret For an overview of how to select surfaces of interest in SumsDB, click here: Selecting Surfaces from SumsDB

2.4.1 WebCaret MenuBar

·         Place the cursor over WebCaret Menubar File: to see its categories

·         Select File: Open Spec Window to see a list of the specfile contents (24 files, 14 types), and an indication of whether the file is currently loaded

The query (?) buttons provide quick access to comment metadata for each file.

·         Close the Spec Control Dialog

File: Download All Files will immediately download the spec file contents if selected.  Do NOT select it now!

·         Place the cursor over WebCaret Menubar: Models to see that nine coordinate files and a volume file are loaded. The currently displayed surface model is shown in bold.

·         Select the FLAT model to see the PALS atlas flat map.

·         Place the cursor over WebCaret MenuBar: Window and note that there are options to open up to 10 WebCaret windows.

·         Select Window: Viewing Window 2. A second window containing a dorsal view of an average fiducial surface will open.

·         Place the cursor over WebCaret MenuBar: Surface. Two options (‘Region of Interest operations’) are available (see Sections 2.12 and 2.15).

-The Refresh option reloads the current WebCaret window.

-The Maximize option increases the WebCaret window size. (Currently it can’t be reversed, so do NOT select this option.)

-The Reset option restores the default view of the currently loaded surface

·         Select Menubar: Model: INFLATED, and close Window 2.

2.4.2. WebCaret Toolbar: standard views, rotation, zoom

The WebCaret Toolbar is similar to that in Caret.

·         Press Toolbar: M for a medial view.

Note: If you still see a lateral view, that is because a glitch is not yet fixed; in the meantime, press Toolbar: L for the medial view.

Toolbar: M, L, A, P, D, V operate as in Caret

·         Press Toolbar: X, to rotate 90° about the screen x axis. Ditto for Toolbar: Y and Z.

·         Press Toolbar: + to zoom in (scale by 1.33).

·         Press Toolbar: – to zoom out (scale by 0.67).

WebCaret does not allow continuous rotation or zooming as is done in Caret, nor does it allow panning

2.4.3 Scene selection

·         Press the Scenes pulldown menu and note that 9 distinct scenes are available for selection

·         Select Scene 2 (Avg MRI (3-slice view)) for a view of the average structural MRI volumes in different slice views (Fig. 2.3).

·         Text Box: Fig. 2.3 Scene 2. Average MRI volumeClick on various locations in one or another of the volume slices.

The slice selection and cursor location will jump to the selected location and a separate Identify window will report the voxel ijk number and the voxel coordinates relative to the stereotaxic origin (AC = anterior commissure).

·         Close any Identify windows that have been opened.

·         Select Scene 3 for a view of probabilistic sulci on the inflated surface (Fig. 2.4).

·         Click on a node and inspect the information provided in the Identify Window

The display format is different from that currently used in Caret, as it includes full information about each column name for paint and probabilistic atlas entries. 

·         Select Scene 4 for a probabilistic map of identified sulci in the 3D volume.

·         Select Scene 5 to view visuotopic areas and Brodmann areal boundaries on a flat map with sulcal depth as an underlay.

2.4.4 Display Control (D/C) Window

·         Press Toolbar: D/C to open the Display Control window, then press the ‘?’ (query) button in the paint row (just to the left of ‘Visuotopic…’.

·         Text Box: Fig. 2.4 Scene 3. Probabilistic sulci on the inflated surfaceClick on the first hyperlink in this window to launch a separate browser window that links to the online journal article (Hadjikhani et al., 1998) that provided some of the data contributing to this map.

·         Close the comment window and the online journal page.

·         Select Scene 6 for a probabilistic map of area 45 (Amunts et al., 2004) plus Brodmann areal boundaries on the inflated surface.

·         Press Toolbar: D/C to refresh the Display Control Window

·         Select Scene 7 for a map of vibro-tactile activation in early blind subjects on the inflated surface

·         Press Toolbar: D/C.

·         Select Metric: MFM –BURTON_04_VibroTactile SIGHTED to see that the activation pattern in lateral occipito-temporal cortex is dramatically different in sighted vs. early blind subjects (same data as in Fig. 1.17A).

·         Press the ‘?’ (query) button in the metric row (just to the left of ‘MFM-BURTON……’) to see metadata, including a link to the online Burton et al., (2004) journal article.

·         Press Toolbar: M for a medial view.

·         Select Metric: MFM –BURTON_04_VibroTactile EARLY_BLIND to see that the activation pattern in medial occipito-temporal cortex also is dramatically different in sighted vs. early blind subjects (same data as in Fig. 1.17B).

·         Select Scene 8 for a map of cortical folding abnormalities in Williams Syndrome (Van Essen et al., 2006) (Fig. 2.5A).

·         Text Box: Fig. 2.5 Scene 8.  Williams Syndrome cortical folding abnormalities in inflated (A) and Very Inflated (B) surfaces.Select Models: Very Inflated, then Toolbar: L to see the same set of folding abnormalities on the very inflated surface (Fig. 2.5B).

·         Click on the red patch in interior frontal cortex to see in the Identify Window (Fig. 2.5C) that the highlighted node (blue) is in a ‘thresh_normal_deeper_t+3’ patch for both the left and right hemispheres in the Williams Syndrome folding abnormalities (RIGHT) and (LEFT) paint columns.

·         Select Scene 9 for a map of stereotaxic activation foci from studies published in the Journal of Neuroscience in 2000.  

2.4.5 Popup block? 

Scene 9 launches multiple WebCaret windows.  If you receive a warning about pop-ups being blocked, then add sumsdb.wustl.edu to the list of trusted sites for which pop-ups are allowed.  Using Microsoft Internet Explorer, select Tools: Internet Options: Privacy: Popup Blocker Settings and add "sumsdb.wustl.edu" to the list of trusted sites.  Mozilla users select Edit: Preferences: Privacy and Security: Popup Windows: Allowed Sites.

·         Click on any activation focus and review the information provided in the Identify Window

At the top of the Identify Window is information about the coordinates of the focus in each of the stereotaxic spaces of the currently loaded average fiducial surfaces (see Section 1.23.4).  There is also a link to the relevant online journal article.

2.5 Additional WebCaret atlas demo’s

Other atlas data sets can be viewed in WebCaret by clicking on the appropriate multi-panel image or the ‘Left’, ‘Right’, or Cerebellum on the View Online (WebCaret) line.  You can explore these later at your leisure.

2.6 SumsDB archive overview

SumsDB contains many types of data that can be navigated and analyzed in a variety of ways.

Data types. SumsDB is promiscuous, in that there are no restrictions on the file types that can be entered.  However, Caret files and certain other file types are handled in customized ways that can prove especially useful.

Archives (*.zip, *.tar.gz, etc) are automatically uncompressed and un-tarred.

Individual Caret files are processed for various kinds of metadata that are used in browsing and searching.

Caret spec files are especially important because they allow for immediate launching of WebCaret as well as organizing complex groups of files.  Spec files listed in SumsDB (in a directory or as  search result) have an adjacent brain icon  that is used to launch WebCaret.  Pressing the brain icon:

              -     Loads the spec file and its contents

              -     Displays the first scene if there is a scene file

              -     Displays the default configuration if there is no scene file. 

Freesurfer and vtk files can (optionally) be converted to Caret file format within SumsDB, thereby permitting immediate WebCaret visualization (Section 2.18).

2.7 Navigating directories and archives

·         Select MenuBar: Directories: Atlases

Text Box: Figure 2.6.  Atlas directory listing.The directory page (Fig. 2.6) contains the following

      -   Instructions along the top for several commonly executed steps:

      -   ‘Apply the Following Action’ options, some of which are  discussed below (Section 2.7.2)

      -   A set of directory actions

      -   A directory listing, indicating that you are looking at the /ROOT/public/ATLAS_DATA _SETS directory.

      -     Several spec files contained in the ATLAS_DATA_ SETS directory.

                      The directory actually contains a much larger number of individual files, but to avoid clutter  the default display shows only spec files.  

 

      Each spec file entry includes the file name, upload data, size, comment on upload, plus several action options to the left.

2.7.1 Spec files in Sums DB

·         Place the cursor over the WebCaret (brain) icon just to the left of the (PALS...WebCaret_DEMO...) spec file to see the ‘visualize surface’ explanation popup.

      Do not press the WebCaret icon at the moment, as this is the same WebCaret demo just covered in Section 2.4.

·         Place the cursor over the disk icon just to the left of the brain icon to see that its function is to download the spec listing (the spec files plus all of the listed files) as a zipped archive.

·         Press the Single File Action pulldown button to the left of the first spec file.

      There are 20 options available (Fig. 2.7A).  The first four are self-explanatory download options. The remaining 16 are to varying degrees self-explanatory and of varying overall utility. Only a few are discussed here.  

Text Box: Figure 2.7.  A. Single file Action options.   B.  Spec file archive text listing2.7.2 Viewing spec file listings

·         Select Single File Action: Details options:  Show Text View to see the text content of the spec file (Fig. 2.7B).  The spec file lists ~30 files, arranged by file type (closed topo_file, etc.).

·         Return to the preceding page (or press Directories: Atlases)

·         For the WebCARET.DEMO spec file, select Single File Action: Show Spec Listing to see an alternative, more flexible way of displaying the spec file listing.

                The downloading icon is present, but there is no brain icon by the individual files because WebCaret is launched only via spec files.

·         Text Box: Figure 2.8. Action options when multiple archives are selected.Place the cursor over the ‘archive’ icon  of any of the files to see that this allows you to download the parent archive, not just the individual file.

·         Press the Single file action next to the first listed file (PALS . . .metric).

            Sixteen options are listed – all but four of those available for spec files.

2.7.3 Downloading checked files

Suppose that you are interested in downloading some but not all of the  files listed within a spec file.

·         Press the buttons under the Select column (far left) for the first 3 files listed

·         Press Apply the Following Actions: Choose Multi-file Action near the top to see a pulldown menu of 10 options that can be applied collectively to the checked files (Fig. 2.8).

                The download checked files option is particularly useful. Note that no action will be taken until you press the adjacent submit button.

2.7.4 Viewing file details

·         Click on the top entry in the Name column (PALS...metric) to see the Detail page about this file (Fig. 2.9).

            The detail page quickly shows you key information about who has read/write permission as well as the contents of the file header. In this case, the file includes URL’s that provide active links to the relevant online journal article.

2.8 Downloading commonly used atlas data sets

·         Press Men Bar: Home (upper left corner) to return to the home page

Many atlas datasets, including the ‘STANDARD-SCENES’ data sets illustrated in Part 1, can be accessed directly from the home page using (i) the ‘Go To Data Directory’ line, or (ii) using the Menu bar: ATLASES option.

·         Press Go to Data Directory: Cerebral (PALS) (under the Human PALS atlas) to view data sets that can be downloaded.

·         Press Menu Bar: Home

·         Text Box: Figure 2.9. ‘Detail’ page for an individual file (metric file) archived in SumsDBPress Go to Data Directory: RIGHT (under the Macaque atlas to see standard data sets for the macaque). These are now based on the standard-mesh F99 atlas described in Part 3.

·         Select Menubar: Directories: Atlases

Data sets in this directory can be downloaded by any of several options:

-   Download icon to the left of individual files or archives;

-   Download and Download (as gzip) options in the Single File Actions pulldown menu;

-   Download (as zip) and Download (as tar.gz) options in the Apply the Following Action: choose multi file action pulldown menu (near top of screen), which applies to all checked files/archives.

2.9 Publication-related data sets.

A growing number of neuroimaging publications include data sets that are contained in SumsDB. These data can be accessed via:

- the Current Publication listing on the home page (Section 2.10)

- the Toolbar: Directories: Publications directory

- links from online journals (see Section 2.19 below)

- search processes initiated within SumsDB (Section 2.12).

2.10 Viewing published data and linking to online journals/figures.

WebCaret and SumsDB allow queries about published data sets that go far beyond simply replicating the figures in a published paper.  The next example starts with data from a recent paper, accessed from Current Publications. It shows how the publication-related data can be efficiently compared to a variety of data, including fMRI data from other studies in SumsDB.

§         Return to the SumsDB home page

§         Select Current Publications: FoxEtAl_PNAS_05 (fourth entry under Go to Download Directory)

§         Click on the WebCaret icon. 

§         The initial WebCaret scene (once data are loaded) shows a panel from Fig. 1 of the Fox et al. (2005) article.  Orange and red regions show fMRI signals that are correlated with the ‘PCC’ (posterior cingulate (precuneus) seed region; blue regions show negative correlations with the same seed region.

§         Press Toolbar: D/C

§         Press the query (?) button on the metric column.

§         Press the link to the PNAS article (http://www.pnas.org/cgi/content/full/102/27/9673/FIG1)

The link takes you directly the relevant figure (Fig. 1) of the online article, which also includes useful figure-specific information in the legend (Fig. 2.10).

Text Box: Fig. 2.10 Figure 2 plus legend from Fox et al. (2005), accessed via a WebCaret/SumsDB study-specific link.

 

§         Close the Comment window and the just-opened online journal browser window to reduce clutter.

§         In the WebCaret main window, select the third scene: Fig. 2 MPF seed. . .

§         Press Toolbar: D/C to refresh the Display Control window.

§         Press the query (?) button on the metric column.

§         Press the link to the PNAS article (http://www.pnas.org/cgi/content/full/102/27/9673/FIG2) and note that the link takes you a different figure (Fig. 2) in the online journal.  Like the preceding example, the legend to this figure provides relevant explanatory information.

The ‘peak focus’ (large green square) visible in WebCaret is not present in the online journal figure, but instead was taken from stereotaxic coordinates in Table 1 and projected onto the PALS atlas as a foci projection file.

§         Select the Fig. 2 Conjunction map scene (ninth from top) to see the map shown in Fig. 2.8A. 

§         Press Toolbar: D/C to refresh the Display Control window.

2.11 Analyses using the Display Control window of currently loaded data.

Suppose that you want to see how the ‘intrinsic network’ pattern revealed in the Fox et al. study compares to the location of various cortical areas. This can be done easily in the current example because the uploaded dataset includes paint files and border projection files that delineate cortical areas by several partitioning schemes.

§         Select Display Control: Paint: Visuotopic + Orbitofrontal (8th from top) to view the fMRI correlation/anti-correlation map in relation to both visuotopic areas and orbitofrontal architectonic areas (Fig. 2.11B). 

Fig. 2.11 Intrinsic network in relation to cortical areas as portrayed in the journal figure (A) and after using WebCaret visualization options to compare to cortical areas (B and C).

 

§         Press Primary Overlay: Paint. Now the visual areas are not obscured by the metric file data, but the relationships between the two sets can be appreciated using the white border contours of the intrinsic network regions. 

§         Click on any node of interest within one of the painted areas to see the node identity for each of the columns in the paint file. 

The format of the Identify Window report shows each column name in the paint file and the node identity according to each column (e.g., Visuotopic + OrbitoFrontal - RIGHT - PALS-B12: OngurEtAl_03_10p). For the metric file, values are reported for all of the metric columns for the selected node.

§         Close any open Identify Windows.

§          Select Display Control: Paint: Brodmann (6th from top) to view the fMRI correlation/anti-correlation map in relation to Brodmann architectonic areas (Fig. 2.11C).

§         Click on a node in the brownish region in parietal cortex (highlighted green node in Fig. 2.11C) and note in the Identify Window that this is area 7 (‘Brodmann.7’ in the Brodmann paint column entry that spans most of the lateral parietal (LP) region outlined by the white border.

§         Close the Identify Window

2.12 Database ROI analyses.

This section illustrates how to query SumsDB for data from other studies that can be appended to the currently loaded WebCaret dataset (Fox et al. 2005).  The searches are intentionally restricted to (i) fMRI data that have been mapped to the PALS atlas and (ii) datasets that have been carefully annotated so that they are useful rather than opaque or confusing.

·         Select Menu bar: Surfaces: Database Regions of Interest Operations

·         Reposition the Region of Interest Search window to the right of the WebCaret window

·         Select Choose Search Atlas: Human-right-PALS-B12 (Currently there are not an ‘ROI-searchable’ data available for the left hemisphere atlas.)

·          Select Choose Search Type: Metric.

·         Select Metric Threshold (low/high) to 2 (low); leave the high at the default of 10

Metric file data are often (though assuredly not always) reported in terms of z-scores or some similar statistical measure.  Hence, a lower bound of 2 is a good initial choice for identifying relevant activation patterns.

·         Press the  ‘+’ button to update the search constraints.

The Selection Method automatically switches to And Selection (Intersection), but this can be changed if desired.

·         Select Choose search: Nodes w/Paint.

·         Select Category Name: Brodmann

Wait a moment for the screen to refresh, as it reduces the list of available names the default (all names in the loaded paint file) to just the names actually in the selected column.

·    Select Area Name: Brodmann.7 (scroll to near bottom)

·                Press the Search button.

After a few moments while the search occurs, a Region of Interest Search Results page will appear, with a list of 20 metric columns meeting the stated criteria, plus information about each data column.

2.13 Format of ROI Search Results.

The search results are displayed in rank order, with the top of the list indicating the metric column having the largest number of  surface nodes meeting the search criteria (Fig. 2.12B). 

In this example, the first entry has a ‘Count’ of 3106 nodes within area 7 having metric value > 2.  

The column name (MFM – RIGHT FOX_05) reveals that these are from the Fox et al. study - data that are already loaded into Caret.

            Other relevant metadata include the ‘owner’ (who submitted this version of the dataset; the date of data submission; any comment provided when the archive was submitted; and a link to the specific metric file containing the column of interest.

            The 20 columns meeting the search criteria are derived from 6 different metric files.

2.14 Importing Search Results into WebCaret

·    Text Box: Fig. 2.12. ROI Search constraints (A) and results (B).Scroll down to the 5th entry (Columns: MFM - BURTON_04_Vibrotactile_EARLYBLIND) which is the first entry that isn’t part of the Fox et al. (2005) study.

·    Press the Import File into WebCaret for this entry button

                 After a moment an ‘Operation Status’ popup will appear, indicating that the import operation is complete. Then it will automatically disappear.

·                Select Display Control: Metric:  MFM - BURTON_04_Vibrotactile_EARLYBLIND from the metric pulldown window.

   The activation pattern (Fig. 2.13A) shows a strong correlation with the intrinsic network pattern previously shown in Fig. 2.11A.

If the white borders have disappeared, press Display Control: Surface Miscellaneous: Toggle Borders.

·    In the Region of Interest Search Results Page, press Import into WebCaret for these additional files from three studies/

           AM vs TM marked by All Act >65 (Beauchamp et al. 03) (entry #6)

MFM-Att and Location (Corbetta et al. 00) (entry #10)

MFM_LOC (Denys et al. 04) (entry #18)

In the Display Control Dialog,

·    Press Primary Overlay: Metric and Secondary Overlay: No Coloring

·    Select Metric: AFM-AllAct: t-stat (Beauchamp et al. 03)

·   Press Toggle Borders if the intrinsic network borders are not visible.

The Human motion vs Tool motion activation from the Beauchamp et al. (2003) study shows a strong correlation with the intrinsic network pattern shown in Fig. 2.11A and Fig. 2.13A.

·   Select the AVERAGE LEFT all_fixation_LalPS column to see the functional correlation pattern associated with the IPS seed (Fig. 2.13C).

These correlations from three different studies are not easily appreciated from simply reading from the literature, because figures of the activation pattern are not displayed in the same way (or at all) in some of the publications. Consider how many additional interesting correlations might be identified if a large (rather than minute) fraction of the literature were comparably accessible.

2.15 Local ROI analyses.

Text Box: Fig. 2.13 Search results from (A) Burton et al. (2006),  (B) Beauchamp et al. (2003) in relation to intrinsic network IPS seed (C).Once the data from other studies have been imported into WebCaret, additional comparisons and analyses can be done using the Surface: Local Regions of Interest Option.

·         Select the AFM-AllAct-T-stat (Beauchamp et al. 2003) metric column

·         Select Surface: Local Region of Interest Operations from the WebCaret window.

·         Select Selection Method: Nodes with Metric

·         Select Threshold (low/high): 4 and 20 and press Submit.  All of the yellow-orange region will now be highlighted in green,

·         Select Selection Method: And Selection (intersection)

·         Select Selection Method: Nodes within border

·         Text Box: Fig. 2.14.  Results of local ROI search applied to Human vs Tool motin (Beauchamp et al. 2003) masked by the Fox et al. (2005) IPS ROI.Select Borders: IPS and press Submit. Only those nodes with the IPS ROI and above threshold in the currently selected metric column are highlighted (Fig. 2.14)

In this way comparisons of complex experimental data from multiple studies can be compared objectively and systematically.

·         Close the Local ROI analysis browser window.

2.16 De novo ROI searches in SumsDB using a standard atlas template.

Suppose you are interested in searching for published fMRI activations that involve a particular region or cortical area and that you wish to initiate this search ‘de novo’ rather than in connection with a published study as in the preceding example.  The next example shows how to search for activations of visual area MT.

2.16.1 Database ROI Search (fMRI data in metric file columns)

·    Return to the SumsDB home page and select  Menu bar: Directories: Atlases

·   Select the HUMAN/ directory, then the fMRI-for-PALS-ROI-SEARCH subdirectory

[Alternatively, link to http://sumsdb.wustl.edu/sums/directory.do?id=6574352]

·    Press the WebCaret icon next to Human.PALS_B12.RIGHT_TEMPLATE_WEBCARET-SEARCHES.73730.spec

This will launch a WebCaret window that provides a useful starting point for SumsDB searches.

The default (first) scene is a lateral view of the PALS inflated right hemisphere. 

·    In the WebCaret main window, press Toolbar: Spec to see a list of the currently loaded files. 

These include various files that are useful for visualization and localization to different cortical areas.  However, there are no metric files (fMRI data) or foci projection files loaded (yet). 

·    Close the Spec dialog window.

·    In the WebCaret main window, press Toolbar: D/C and drag the Display Control to the right.

·    Select Display Control: Paint: Visuotopic from the pulldown menu (current reading AVERAGE-MED-WALL…) to see the location of MT+ in red, along with other visual areas.

The paint column has been selected as a secondary overlay, so that the metric data resulting from the search can be represented on top as a primary overlay. 

·    Select Menu bar: Surfaces: Database Regions of Interest Operations

·    Reposition the Region of Interest Search window to the right of the WebCaret window, as in Fig. 2.15.

·    Select Choose search atlas: Human-right-PALS-B12

·    Press the reset button to clear out previous search constraints.

·    Select Choose search type: Metric.

·     Select Metric Threshold (low/high) to 2 (low); leave the high at the default of 10

·    Press the  ‘+’ button to update the search constraints.

·    Select Choose search: Nodes w/Paint.

·    Select Category Name: Visuotopic

Wait a moment for the screen to refresh.

·    Select Area Name: Visuotopic.MTplus 

·    Press the Search button.

Text Box: Figure 2.15  WebCaret view of PALS atlas surface and SumsDB Region of Interest Search window.After a few moments, a Region of Interest Search Results page will appear, showing results for 14 metric file columns meeting the stated criteria.

2.16.2 Using ‘Show Nodes’ to view ROI results

In this example, the first entry has a ‘Count’ of 314 nodes within MT having metric value > 2, (AFM - Attend location (Corbetta et al., 2000)

The 14 columns meeting the search criteria are derived from 5 different metric files.

·    In the top entry, press Show nodes in WebCaret.

·    Press Toolbar: Refresh (or Display Control: Refresh Model) to see the nodes meeting the search criteria highlighted in green on the PALS atlas surface.

The highlighted nodes almost completely encompass MT+.

·    Press Import: Import file into WebCaret for the top entry (MFM – RIGHT-Attend location (Corbetta et al., 2000)

·         Press the D/C button on the main window menu bar to refresh the Display Control window contents..

The WebCaret Display Control window now includes a metric file entry.

·    Press the Display Control: Metric: Primary Overlay button.

The WebCaret main window (Fig. 2.16, left panel) will now display an fMRI activation pattern from an ‘attend to location’ task in a study by Corbetta et al (2000).

·    Text Box: Fig. 2.16. Search results in WebCaret plus linked publications.Press the blue ‘?’ (query) button just to the left of the metric column name (MFM Attend location (Corbetta et al., 2000)). 

The popup dialog will show the metadata comment associated with this particular metric column (Fig 2.16 lower middle panel).  It includes various types of information.  Of particular utility are the hyperlinks to two publications associated with this data set, both as PubMed links and as direct links to the online journals.

·    Press the http://dx.doi.org/doi:10.1038/73009 link in the comment file.

                         This should launch another browser window that takes you directly to the Corbetta et al. (2000) Nature Neuroscience online article (Fig. 2.12, far right panel).  (If that doesn’t work, try the PubMed link (http://www.ncbi.nlm.nih.gov/entrez/….) instead).

·    Close the Comment popup window and the online publication window. 

2.17 Foci Searches

Neuroimaging results reported by the stereotaxic coordinates of the centers of activation foci are inherently complementary to the complex patterns revealed by metric files (Sections 1.26, 1.27, 2.16).  SumsDB and WebCaret capitalize on some of the inherent advantages in the discreteness of foci.

·                Link to SumsDB in your browser window (http://sumsdb.wustl.edu/sums/)

2.17.1 Foci Study Searches

·                Select Menu Bar: Browse/Search: Foci Study Search

Suppose you want to search for stereotaxic foci associated with a particular author (e.g., Steve Rao).

·                Enter Author: Rao, then press Search.

After a few moments, the Foci Study Search Results page will appear, showing results for 1 study (as of September, 2006, based on J. Neuroscience publications 1997 through 2002 that include several thousand foci.

Listed under the Detail column is information about the title, authors (Leveroni et al.), citation, URL (link to the online journal), keywords, plus access to a tabulation of the data and to the dataset.

·                Press Link to Cell Data near the bottom.

The Foci Study Detail page will list the focus name and stereotaxic coordinates (in AFNI space, as indicated in the Results page for this study), plus several other types of data.

NOTE: These data can be cut and pasted into an Excel spreadsheet, which can be useful for additional offline analyses. 

·                Press Link to Archive at the bottom.

The foci projection data files containing the results for this study will be listed, available for downloading.  [It is not yet possible to import these directly into WebCaret, as was just done for metric files, but this capability is planned.]

2.17.2 Foci Data Searches

Suppose you want to search for stereotaxic foci within a certain distance from a specified location in the cortex.  (If you knew the desired coordinates already, you could skip the next four instructions.)

·         Return to the SumsDB home page and select  Menu bar: Directories: Atlases

·        Select the HUMAN/fMRI-for-PALS-ROI-SEARCH subdirectory

 [Alternatively, link to http://sumsdb.wustl.edu/sums/directory.do?id=6574352]

·         Press the WebCaret icon next to PALS_B12.BOTH.WEBCARET-STEREOTAXIC-FOCI-SEARCH.73730.spec

This will launch a WebCaret window useful for identifying stereotaxic coordinates around which foci searches can be generated.

The default (first) scene is a lateral view of the FLIRT average fiducial surface, with visuotopic and orbitofrontal areas displayed.

·                Click on a location near the center of area MT+ (the red area in occipito-temporal cortex.

The reported stereotaxic coordinates in the Identify Window will be approximately (+44, -75,  0). 

(You could start here if you already knew the coordinates for your search center.)

·                Select Menu Bar: Browse/Search: Foci Data Search

·                Enter X: 47, Y: -75; Z: 0; Distance: 15, then press Search.

After a few minutes this will generate a Foci Data Search Results page reporting at least 64 foci within 15 mm radius (not a bounding box) of the specified stereotaxic coordinates 47, -75, 0).  These foci (from 5 studies)

            The coordinates of each focus are reported, as well as various other metadata.

·         On the far right ‘Study’ column, press the second entry from the top (‘Human Brain Regions.. . . ‘ for the Peuskens et al. study) This will show key metadata for this study, including a link to the online publication.

·         Press Cell Data: Link to Cell Data to see the coordinates of all the foci (~100) reported in this study.

·         Return to the previous web page

·         Press Link to Archive to see

This shows the archive in which the selected focus is stored

·         Select  Single File Action Show Parent to see the spec file (PALS_B12.BOTH-HEMS.For-STEREOTAXIC-FOCI-ANALYSES.73730.spec) in which this foci projection file is embedded foci projection file

·         Press the WebCaret icon .

·         Select the fourth scene: J. Neuroscience...(FLIRT Avg Fiducial) to view all of the foci in this file

·         Select Menubar: Search Results: Foci Data Search Results to return to the list of 21 foci matching the search query.

[Note – a planned enhancement will allow direct importing of foci data search results into a WebCaret application]

2.18 Viewing FreeSurfer files converted to Caret

·         Press MenuBar: Directories

·         Select FREESURFER_DEMO_CASE-FH/directory

This directory contains four files in FreeSurfer format (*.asc) plus a Caret spec file that was generated within SumsDB by converting these files (2.17A)

·         Text Box: Figure 2.17  FreeSurfer demo directory and individual surface viewed in WebCaret after file conversion within SumsDB.Press the WebCaret icon

An inflated surface in the default dorsal view will appear after a moment

·         Press Toolbar: L for a lateral view (Fig. 2.17B)

·         Select MenuBar: Models: rh_smoothwm.asc.coord, then press Toolbar: L for a lateral view of the gray-white surface (Fig. 2.17C)

·         Select MenuBar: Models: rh.pial.asc.coord, then press Toolbar: L for a lateral view of the pial surface (Fig. 2.17D)

2.18.1 Converting FreeSurfer files to Caret format

·         Check the Select button on rh.inflated.asc, then select Choose Multi-file action, Convert-FreeSurfer Files to Caret

·         Press Submit

In a moment a new screen will inform you that you do not have permission to do this operation

If you were logged on and had appropriate read permissions, this processing would be successful.

2.19 Accessing SumsDB via online journal articles

Text Box: Fig. 2.18. (A) Lateral view in WebCaret of two normal and two WS fiducial surfaces from Fig. 1 of Van Essen et al. (2006). (B) Medial view of the same four cases generated in WebCaretA growing number of online journal articles.  (i) contain data currently in SumsDB, and (ii) contain links within the publication that allow easy access to these data.  To illustrate these links, go to the Sums DB home page

·         Press Current Publications; Link to Paper: Full text article next to the topmost entry (Van Essen et al.  2006. )

·         In the browser window that opens up, scroll to Figure 1 and press the link to SumsDB at the bottom of the legend.

·         Press the WebCaret icon next to the only spec file (Human.PALS.VE...).

In the WebCaret window, the first scene replicates panels A-D of Fig.. 1 in the journal article, namely lateral view of two normal (control) individuals (Windows 1, 2) and two Williams Syndrome (WS) individuals (Windows 3, 4).

·         Resize and reposition the windows as in Fig. 2.18A.

·         Press Toolbar: M in each of the four windows to see medial views of each hemisphere (Fig. 2.18B).

This provides information simply not available in the published study.

·         Text Box: Fig. 2.19. List of sulcal depth maps available in the Display Control pulldown menu (A) plus a flat map representation of sulcal depth in an individual not illustrated in the paper.Select the last scene (Fig. 1N-Q) to view sulcal depth maps of the same two normal and two WS individuals after registration to PALS an displayed on the atlas flat map.

·         Close all but the main window.

·         Press Toolbar: D/C

·         In the Display Control dialog, press the shape pulldown menu and note that sulcal depth maps are available for all 13 controls (NIL) and all 16 WS subjects (Fig. 2.19A).

·         Select and view as many individual sulcal depth maps as you care to see (e.g. to ascertain where the 17 significant folding abnormalities in the right hemisphere are located).

2.20 Basic Archive Search

·         Select Browse/Search: Basic Archive Search

·         Enter Filename: PALS

·         Select File type: Spec

·         Press Search

In a moment you will see that a large number of spec. files (>100) that contain PALS in the title are available for public access (viewing and download)

Many other searches can be carried out in this general way.

2.21 Tutorial datasets and documents.

·         Select Directories: Tutorials.  More than 20 tutorial datasets are available

              At the top of the list is the current CARET_TUTORIAL_SEPT_06 tutorial

              Many tutorials are available, some for WebCaret but mostly for Caret.  In general, each includes a text document (pdf) containing instructions, plus a dataset that can be downloaded. 

·         To identify tutorial documents that can guide you through these datasets, select MenuBar: Browse/Search; Basic Archive Search

·         Select File type: pdf, and press search.

This will display a list of at least 14 pdf documents, representing tutorials from 2002 onward. Any of these can be downloaded, and the documentation will tell you which datasets are needed.

2.22 Options requiring logon

You will need an account and will need to log on in order to view or download data having restricted access and in order to upload data to SumsDB.

2.22.1 Navigating private datasets

You will need a regular SumsDB account to submit data or to non-public data sets shared among investigators (see 1).

§         Click on the Logon (in the upper left sidebar) and login as caret_tutorial (password: pals_rules).

                  Note that this is a temporary account.  You can always access SumsDB as public, but to log on in the future you will need a regular individual account – see 2.17 for details.

2.22.2 Uploading data

Note that the Menu Bar now contains an Upload option that was not present prior to logon

·         Select Upload: Submit Data

·         Press Choose File to bring up a window that allows navigation of your full directory structure.

·         Select Upload: Submit Data Applet. Read the Status: INFO at the bottom.

SumsDB accounts are available to neuroscientists who wish to submit brain-mapping data to SumsDB or to access private data sets made available by other SumsDB users. Each investigator needs a separate account, in order to insure compliance with the SumsDB User Agreement and HIPAA regulations.

To obtain a SumsDB account and an associated Code Access Agreement, select Submitting data

2.22.3 Code Access Agreement (CAA) and HiPAA constraints

SumsDB contains neuroimaging data from many species, including humans. Human data sets entered into SumsDB must comply with HIPAA regulations. Specifically, human data sets must be de-identified and must be covered by a Code Access Agreement to insure that PHI (personal health information) is not included in data submitted to SumsDB or otherwise provided to the Van Essen laboratory. De-identified data sets in SumsDB conform to Washington University policy, in which facial information in structural MRIs is not considered to be one of HIPAA's 18 identifiers.

The Code Access Agreement must be signed and faxed. Multiple data sets from a given investigator can be covered by a single Code Access Agreement.

2.23 Establishing a local SumsDB server.

Currently the only SumsDB serve is situated at Washington University (on a linux cluster in the Electronic Radiation Laboratory).  SumsDB is designed to allow a distributed set of ‘federated’ databases in which multiple sites exist, and allow local data storage combined with searching and selective data sharing across sites.  Investigators interested in establishing a local SumsDB databases should contact sumsdb@brainvis.wustl.edu

--- End of Part 2


Part 3. Macaque Atlases (‘F99’, ‘F6’ and ‘PHT’) and Monkey-Human Comparisons.

 

This section illustrates how to visualize data on macaque cerebral cortex and to make objective comparisons between monkey and human cortex. 

Standard-mesh macaque atlases.  This tutorial introduces new versions of three macaque atlases, each represented in a 73,730-node standard-mesh that allows concurrent visualization of all three atlases (and both left and right hemispheres):

-          the F99 atlas (Case F99UA1), from a rhesus macaque provided by N. Logothetis

-          The F6 atlas (a population-based macaque atlas based on six fascicularis macaques)

This atlas, developed by J. Vincent, G. Patel, and A. Snyder, is particularly useful for monkey fMRI studies.

-          The PHT atlas (Paxinos, Huang and Toga, 2000) generated from drawings of coronal histological sections of a single fascicularis macaque.

The major focus is on the macaque F99 atlas. The next section covers (i) cortical geography and coordinate systems; (ii) partitioning schemes; (iii) probabilistic and fuzzy representations; (iv) connectivity data; (v) fMRI data.

 

·         Change to the MACAQUE/ directory.

·         Enter caret to launch the Caret application.

·         Text Box: Fig.  3.1.  Scene 1. Macaque F99 atlas, fiducial surfaceSelect the Macaque.F99RIGHT.DEMO.73730.spec file.

·         Press the Load Scene(s) button.

3.1 Macaque Geography.

·         Select Scene 1: Fiducial surface, lateral view for a simple start-up view (Fig. 3.1).

·         Press the Model pulldown menu and note that three other surfaces plus the MRI volume are loaded and available for immediate viewing in the main window or in a new window.

·         Select Page Selection: Overlay/Underlay – Surface and note that the sulcal depth is selected as the underlay.  A paint file is loaded but not selected.

·         Select Page Selection Scene, then select the Scene 2: Flat, Fiducial (Lat), Very Inflated (dorso-lat); sulcal depth for a view of three surface configurations (Fig. 3.2).

The fiducial surface is convenient to view in a standard lateral view.  The very inflated surface is in a dorso-lateral view that conveniently allows visualization of the intraparietal sulcus as well as lateral temporal regions.

·         In Window 3,  press Toolbar: L for a strictly lateral view of the very inflated surface.

·         Text Box: Fig.  3.2.  Scene 2. Flat, fiducial (lateral), and very inflated (dorso-lateral) surfaces.  Press : Show selected scene (with the second scene still highlighted) to restore the dorso-lateral view of the very inflated surface.

·         In Window 3,  press Toolbar: Y twice for a ventro-medial view that is rotated 180° and thus complementary to the preceding dorso-lateral view.

·         Select Scene 3: Flat, Very Inflated (dorso-lateral; ventro-medial) for concurrent views of the two complementary very inflated surfaces.

If you find a different combination of surface configurations and views to be useful in one or another ongoing project, recall that it is easy to (i) generate your own customized views; (ii) save them as a scene; (iii) save a combination of scenes (by addition and deletion) as your customized scene file; (iv) create your own spec file from the scene file; and (v) copy this spec file and associated data files to a suitable working directory.

·         Text Box: Fig.  3.3.  Scene 4. Lobar-cuts flat map uplus very inflated surfaces (dorso-lateral, medio-ventral viewsSelect Scene 4: LOBAR Flat, VeryInflated (dorso-lateral, ventro-medial to view a flat map in which the cuts are placed differently, leaving the frontal and occipital lobes with cuts near their margins (Fig. 3.3). 

This is analogous to the lobar-cut human flat map (Fig. 1.11); it can aid in viewing data that are spread across the frontal and/or occipital lobe.

·         Click on various locations on the lobar flat map and see where the highlighted nodes are on the inflated surfaces, in order to get better oriented to this flat map layout.

Information about spatial coordinates are reported in the Identify Window; these are discussed further in Section 3.6 (Spherical coordinates and multiple stereotaxic spaces).

·         Press Unload All Files Except Scene

·         Select Scene 5: Flat, Fiducial; Coronal MRI for a view of two surfaces plus a coronal MRI slice with the right hemisphere surface contour overlaid (Fig. 3.4).

Text Box: Fig. 3.5.  Cortical lobes and ‘geography blend’Text Box: Fig. 3.6.  Scene 7. Identified sulciText Box: Fig. 3.4.  Scene 5. Flat, Fiducial, Coronal MRI views.Recall the various options for clicking on locations of interest in any window and highlighting the corresponding location in other windows.

 

·         Select Scene 6: Lobes + geo-blend on Flat, Fiducial, Inflated for a view of cortical lobes, with buried cortex shown as a blended ‘geo-blend’ underlay (Fig. 3.5).

The degree of geography blending is controlled on the Page Selection: Overlay-Underlay-surface page

 

·        Select Scene 7: Identified Sulci... to see 13 sulci individually colored (Fig. 3.6).

·        Press the appropriate color bar in the Paint Color Key to highlight any sulci of interest.

·        Press Toolbar: Spec: Misc and open the Vocabulary Files: Macaque.Sulci.Vocabulary file.

·        Click on Paint Color Key: SUL.AS to see its full name plus additional metadata (including a link to the online publication). 

·         Press various other sulcal abbreviations to bring up vocabulary information.

3.2 Cortical areas and functionally specialized regions.

Many different partitioning schemes for macaque cortex are in widespread use.  The F99 atlas dataset contains 13 distinct schemes covering part or all of the hemisphere that can be viewed in a variety of formats.

·        Select Page Selection: Paint

·        Select the LVE_00 column to see the Lewis & Van Essen (2000) partitioning scheme for visual areas, then press the Paint Color Key: Update (Fig. 3.7).

·        Press Toolbar: Spec: Misc, open the Vocabulary Files: Macaque.CorticalAreas.Vocabulary file, and press Append.

·        Click on Paint Color Key: LVE00_2 to see its full name plus additional metadata (including a link to the online publication). 

·        Click on the color bar next to LVE00_2 to see its location highlighted.

·        Text Box: Fig.  3.7.  Scene 8. Lewis and Van Essen (2000a) partitioning scheme with borders. - Click on any other color bars or area abbreviations of interest to ascertain their location and/or full identity.

·        Select the next 10 columns (from Felleman-VE to Preuss & Goldman-Rakic) one after the other to see maps of an additional  11 published partitioning schemes for part or all of macaque cortex.  (Some maps include multiple schemes that each span a different subregion of the hemisphere.)

·        Update the Paint Color key whenever you want to see the area names and colors.

·        Click on any other color bars or area abbreviations of interest to ascertain their location and/or full identity

·        Click on any location of interest on one of the cortical surfaces to see the areal assignments in the Identify Window for all of the loaded paint columns (bold type indicates the currently viewed paint column).

·        Press Identify Window: CID to clear any identified nodes from the surface displays.

·         Select Page Selection: Scenes, then select Scene 8: Lewis-VE areas, borders on Flat, Fiducial, scene for a view of cortical areas by the Lewis & Van Essen (2000a) partitioning scheme (Fig. 3.7).

Including the areal boundaries provides more distinct and aesthetic maps

·         Click on the black color bar next to any of the borders to see it highlighted

·         Press Page Selection: Border: Override border colors with area colors and press Border Color Key: Update

·         Text Box: Fig.  3.8.  Scene 9. Lewis & Van Essen (2000) areas on flat map, fidicual surface, and coronal slice, with node highlighted in MT.  Select Page Selection: Paint, select the Brodmann paint column, and press Paint Color Key: Update to see colored Lewis & VE boundaries overlaid on colored Brodmann areas.

·         Select Page Selection: Scenes and Scene 9 (Lewis-VE areas on Flat, Fiducial; Coronal MRI) for a view of areal boundaries of Lewis & Van Essen (2000a) in the MRI volume (bilaterally) as well as on the surface (Fig. 3.8).

            Several other areal partitioning schemes can be viewed as paint volumes, but they must be opened separately (Toolbar: Spec: Volume Files – Paint: option). 

·          Select Scene 10: Ferry et al. (2000) for a map of orbitofrontal areas mapped from case om43.R in Price lab (Fig. 3.9) and displayed non-standard views of fiducial and very inflated surfaces

N.B.  This map of macaque orbitofrontal areas differs significantly from previously orbitofrontal maps (cf. Van Essen, 2005) and is more accurate (owing to improvements in surface-based registration from flat map via spherical registration).

3.3 Probabilistic maps and fuzzy transitions.

·         Select the previously viewed Scene 8: Lewis-VE areas, border on Flat, Fiducial, Very Inflated scene

The Lewis & Van Essen scheme currently in view is based on maps generated from 5 individuals and can accordingly be viewed as a probabilistic map that reflects individual variability.

·         Select  Scene 11: Lewis-VE probabilistic map + boundaries on Flat, Fiducial, VeryInflated scene for a probabilistic map of the same Lewis & Van Essen (2000a) areas.

·        Click on various nodes to see the areal assignment in each of the five hemispheres contributing to the atlas. 

In each individual, areal identities were assigned only to the ‘core’ region for each area; transitional regions between identified areas are unassigned (‘???’ in the Identify Window). 

·         Text Box: Fig.  3.9.  Scene 10. Orbitofrontal areas (Ferry et al. 2000) from anteroventral, medial views of fiducial surface, anteromedial view of very inflated surface.Select Scene 12: Lewis-VE (areal estimation) + borders on Flat, Fiducial, VeryInflated for a different representation of gradual transitions between areal boundaries.

·         Click on a node near an areal boundary to see the fractional assignment to different areas.

These assignments are based on distance from the designated boundaries in the border projection file they were not computed directly from the probabilistic atlas file viewed in the preceding scene.  

·         Select Scene 13: Modalities. . . for a view of different functional modalities.

·         Select Scene 14: Probabilistic visual area clusters on Flat, Fiducial, VeryInflated for a view of probabilistic visual areas (Fig. 3.10).

Text Box: Fig.  3.10.  Scene 14. Visual area clusters (probabilistic atlas map) + Lewis and Van Essen (2000a) area boundaries  The 10 different schemes for parts or all of visual cortex were combined into a visual area cluster map, shown in various degrees of shading according to the consistency across schemes. Note in particular that the infer temporal areas are all shaded blue and the posterior parietal areas are shaded yellow.

Text Box: Fig. 3.11.  Scene 15 Area VIP connections (Lewis and Van Essen 2000b) + Lewis and Van Essen (2000a) area boundaries.  This entailed loading a ‘probabilistic atlas’ file and also a different area color file (MACAQUE.AREAS.VISUAL.CLUSTERS.areacolor) compared to previous scenes.

·        Click on a node in the yellow region (as in Fig. 3.10) to see the identity of parietal areas at this location by various schemes.

3.4 Viewing connectivity data.

·        Select Scene 15: VIP connectivity + Lewis-VE borders on Flat, Fiducial, Inflated for a view of cortical connections from a retrograde tracer injection in area VIP (Lewis & Van Essen, 2000b) plus areal boundaries of Lewis & Van Essen (2000a) partitioning scheme (Fig. 3.11).

·        Select Page Selection: Metric: Selection

·        Select the deformed AIP (+7b) injection then the deformed MSTdp in column to see retrograde labeling patterns from two additional injections registered to F99 atlas.

·        Click on various nodes within the retrogradely labeled patches. The readout from the Metric column in the Identify Window is in log10 units (e.g., a value of 4 indicates 10,000 labeled cells/mm2)

·        Select the deformed injection sites column to see the locations of the three injection sites (plus some leakage along injection tracks).

·         View as many additional connectivity data in this file as interest you.

3.5 Monkey fMRI data

·         Press Scene: Unload All Files Except Scene.

·         Select  Scene 16: fMRI (objected-related activation) on Macaque.M3 MRI scene (Fig. 3.12)

·         Select  Scene 17: fMRI (objected-related activation) on Macaque F99 Flat scene (Fig. 3.13)

                   

Fig.  3.12. Scene 16. Objects vs. scrambled                                    Fig.  3.13. Scene 17. Objects vs. scrambled

objects (volume slices).                                                                      objects on surface maps

3.6 Spherical coordinates and multiple stereotaxic spaces.

Multiple stereotaxic atlases for the macaque exist for the macaque, just as for the human brain. Commonly used macaque atlases include the Paxinos, Huang, and Toga (2000) atlas (PHT00), the Martin-Bowden atlas (ref), and the macaque F99UA1 atlas (Van Essen, 2002).  Here, we provide standard-mesh (73K-node) representations for all three of these atlases, thereby facilitating comparisons of data obtained or analyzed in different spaces.

3.6.1 Macaque F6 atlas.

·         Select Scene 18 (Macaque F6 MRI (3-slice),  Fiducial Lat, Med (AC-origin)) to see the F6 volume plus lateral and medial views of the right hemisphere fiducial surface (Fig. 3.14)

·         Text Box: Fig. 3.14.  Macaque F6 atlas (volume-average of 6 individual fascicularis macaque MRI scans), in volume-slice views and fiducial surface (lateral, medial).Select Page Selection: Overlay/Underlay Volume and press the query button (?) next to Anatomy: Macaque.F6.LR to see information about this atlas.

The F6 population-average MRI atlas was generated from six individual MRI volumes registered to a target whose dimensions match the Martin-Bowden (2000) atlas, which was an individual M. fascicularis that was sectioned postmortem.

3.6.2  Comparing the F99, F6, and PHT00 macaque atlas surfaces.

·         Select Scene 19 (F99, F6, PHT00 Fiducial Lateral, with scales) to see lateral views of all three atlas fiducial surfaces, with axes displayed (1 cm scale bar intervals) (Fig. 3.15A).

The PHT00 atlas is from an individual rhesus macaque, reconstructed from a series of coronal histological sections.

F99 atlas is from a single rhesus macaque (body weight unknown), scanned at 0.5 mm resolution. 

The F6 population-average MRI atlas is made from six individual MRI volumes registered to a target whose dimensions match the Martin-Bowden (2005) individual-hemisphere.  

·         Text Box: Fig. 3.15.  Standard-mesh fiducial surfaces of F99, F6, and PHT macaque atlases from lateral (A) and medial (B) views.Select Surface: Information to see the dimensions of the F99 atlas fiducial surface along x, y, and z axes.  The total length (y extent) is about 79 mm. 

·         In the Surface: Information: Surface pulldown menu, select the F6 fiducial surface and note that its total length is much smaller (62 mm).  Select the PHT00 fiducial surface and note that its length is in between (73 mm).

The individual hemispheres contributing to the F6 atlas were on average about 10% longer than the  Bowden-Martin individual atlas hemisphere, based on the values of the affine transformations provided in the volume comment file.

·          Click on a node anywhere on any surface to see the degree of geographic correspondences in the highlighted nodes in each atlas surfaces.  Information about stereotaxic coordinates for the fiducial surfaces in all three spaces (F99, F6, and PHT00) is reported in the Identify Window, along with the latitude/longitude (spherical coordinates) obtained from the F99 atlas.

Other types of node-specific information contained in the currently loaded files (cortical areas, etc.) are not displayed because they are currently de-selected; this can be easily changed using the various buttons in the Identify Window menu bar.

·         Select Scene 20 (F99, F6, PHT00 Fiducial Medial, with scales) to see medial views of all three atlas fiducial surfaces, with axes displayed (1 cm scale bar intervals) (Fig. 3.15B).

3.6.3  Standard scenes for ongoing analyses.

·         Select File: Open Spec File: Macaque.F99UA1.RIGHT.STANDARD-SCENES.73730.spec.

·         Press the Load Scene(s) button, then press the ‘New Spec Only’ button.  The scene file contains 17 scenes similar or identical to those just viewed earlier in Part 3, but without the numbering

·         (Optinal) If you wish to quickly review these scenes, qress the Check All Scenes button and then Continue and OK in the popup windows for a quick review of all scenes.

3.7 Left hemisphere and dual-hemisphere data sets.

The macaque brain lacks prominent left-right asymmetries like those found in humans (cf. Section 1.31.1).  Nonetheless, the two hemispheres are not completely identical in any individual, and it is sometimes preferable to view data on a left hemisphere atlas.  The macaque F99 left hemisphere was segmented, reconstructed, then converted to the same standard-mesh representation as the right. 

The target landmarks for registration to the standard-mesh were generated by a process similar to that for the human PALS_B12 atlas (Van Essen, 2005a) that avoided a bias for either the left or right hemisphere.  Twenty-six consistent geographic landmarks were drawn on the F99 left and right flat maps, then projected to the distortion-minimized left and right hemisphere spherical surfaces (after spherical multi-resolution morphing to reduce distortions).  The left hemisphere landmarks were mirror-flipped, then averaged with the right hemisphere landmarks, yielding a set of 26 left-right average landmarks.  The left and right hemispheres were then registered to these average spherical landmarks.  As a result, the standard-mesh (resampled to 73,730 nodes) left and right hemispheres are in point-by-point correspondence, within the reliability allowed by the choice of geographic landmarks

Most of the experimental data in the F99 atlas regarding areal partitioning were derived from a mixture of left and right hemisphere analyses and accordingly can be displayed without respect to hemisphere of origin.

3.7.1 Standard scenes for left hemisphere

·         Select File: Open Spec File: Macaque.F99UA1.LEFT.STANDARD-SCENES.73730.spec.

·        Press the Load Scene(s) button, then press the ‘New Spec Only’ button.  Note that the scene file contains the same 13 scenes previously shown for the right hemisphere, except that LEFT is substituted for RIGHT in each scene. 

·        Select the first scene for a standard left hemisphere view.

·        Press the Check All Scenes button and then Continue and OK in the popup windows for a quick review of all scenes.

3.7.2 Standard scenes for concurrent viewing of both hemispheres

·        Select File: Open Spec File: Macaque.F99UA1.BOTH.For-ANALYSES.73730.spec.

·         Press the Load Scene(s) button, then press the ‘New Spec Only’ button.  The scene listing is similar to the preceding individual-hemisphere scenes,  except that generally only a single view is provided for each hemisphere in order to avoid over-proliferation of windows.  (But of course, the user can add windows to taste.)

·         Select the first scene for a view of left and right hemisphere fiducial surfaces.

·         Press the Check All Scenes button and then Continue and OK in the popup windows for a quick review of all scenes.

·         Quit Caret.

 

End of Part 3


 

Part 4. Macaque-Human comparisons. 

A landmark-based, surface-based approach provides a powerful general way to explore comparisons between species and to evaluate various candidate homologies (Van Essen 2005c; Van Essen et al., 2005).

4.1 Concurrent viewing of macaque, human surfaces (pre-registration)

·         cd to the CARET_WashU_SEPT-06/COMPARE_MACAQUE_HUMAN/ directory.

·         Launch caret5 and select the COMPARE_PALS_MacaqueF99.73730.spec file.

·          press Load scene(s)

·         Drag the Caret main window to the upper left corner of your computer screen (to provide adequate space for the four windows about to open), then open Scene 1: LANDMARK areas on Macaque, Human Fiducial, VeryInflated (LATERAL, RIGHT).

This scene shows the macaque atlas fiducial surface in the main window and the human PALS average fiducial surface in Window 2, plus the macaque and human very inflated surfaces in windows 3 and 4.  The painted regions on each surface represent ‘Landmark’ areas known or strongly suspected to be homologous in the two species (e.g., primary sensory, motor areas all identified by abbreviations in the Paint Color key.

In Window 2 (human average fiducial surface), click on a node near area MT+ (red patch near the occipito-temporal junction).  The highlighted node in the macaque surfaces does not lie in area MT, but rather in or near area V1 (purple area) as in Fig. 4.1.

This is because these two maps are not (yet) in register – that comes next!  (The two surfaces can be viewed concurrently because they are each represented by an appropriate within-species 73730-node standard mesh.  However, this does not achieve appropriate between-species registration unless and until an explicit registration process is carried out.)

·         Open Scene 2 (MEDIAL view - LANDMARK areas on Macaque, Human Fiducial, VeryInflated) to see a corresponding set of medial views of the landmark areas.

·         Click on a node near the human frontal pole in Window 2

     The highlighted node in the macaque surface lies substantially ventral and posterior to the frontal pole, i.e. seriously non-corresponding (Fig. 4.2)

·         Open Scene 3: FLAT Macaque, Human - LANDMARK areas to see all of the painted landmark regions on both species.

·         Open Scene 4: Core-20- LANDMARK contours: macaque flat map + Image of human flat map (Fig. 4.3)

    

Text Box: Fig. 4.1.  Scene 1 Landmark areas on macaque F99, human PALS surfaces
.Text Box: Fig. 4.2.  Scene 2. Medial views of landmark areas.

The 20 contours (borders) drawn along the landmark areas provide the explicit constraints used in the interspecies registration process.  The human landmark contours are shown in an image window rather than an active Caret window because Caret does not currently allow window-specific displays of different border sets.

Note that some landmark areas (e.g. MT, A1) are bounded by multiple landmark contours, whereas others share a single contour between two or more areas.

·         Open Scene 5: Human PALS Inflated; Macaque Fiducial (Standard-mesh + Registered-mesh Core-20-LDMK-VE).

This shows the inflated PALS atlas surface plus two seemingly identical views of the macaque fiducial surfaces (Fig. 4.4).  The macaque surfaces are in fact very different, as demonstrated below:  (i) the ‘standard-mesh’ macaque F99 surface (same as in Part 3), and (ii) a ‘PALS-registered F99-mesh’ surface that establishes a principled set of correspondences between nodes on the macaque and human surfaces.

The registered-mesh macaque surface is labeled by a code (Core-20-LDMK-VE) in which Core-20 refers to the Core-20 landmark contours used as constraints (cf. Scene 4; Fig. 4.3); VE refers to the investigator responsible for this particular choice of landmarks and registration parameters.

Text Box: Fig.  4.4.  Scene 5. Landmark areas on PALS inflated surface, macaque ‘standard=mesh’ + PALS-registered mesh’ fiducial surfaces
.     

Text Box: Fig. 4.3. Scene 4. Landmark contours + areas on macaque, human flat maps side by side.
.

·         Open Scene 6: ID node - Human Inflated; Macaque Fiducial Standard-mesh + Registered-mesh (Core-20-LDMK)

As seen in Fig. 4.5, a node highlighted at the lateral margin of the occipital operculum (the foveal representation in V1) in the PALS-registered F99-mesh maps to the human foveal representation at the occipital pole (i.e., at a functionally corresponding but geographically very different location).  In the standard-mesh macaque surface, the highlighted node is in a different location both geographically and functionally.  

·         Open Scene 7: Occipital Pole tiling, ID node - Human Inflated; Macaque Fiducial Standard-mesh + Registered-mesh (Core-20-LDMK)

In this wire-frame tessellation of the same three surfaces (inflated PALS, macaque standard-mesh and registered-mesh fiducial surfaces), the marked differences in the tiling of the macaque occipital cortex are apparent (Fig. 4.6).

          

         Fig. 4.5.  Scene 6. Identified node on PALS plus two                  Fig. 4.6. Scene 7. Differences between standard-mesh and

         macaque F99 meshes                                                                     PALS-registered mesh tessellation of occipital cortex.

 

4.2 Quantifying human-macaque cortical expansion ratios.

·         Open Scene 8: Sulcal depth-macaque (Main) deformed macaque (Window 2), PALS average depth (Window 3), as in Fig. 4.7

This shows a map of sulcal depth on the macaque flat map (Main window), and after deformation to the PALS surface (Window 2). For reference, Window 3 shows the average sulcal depth map for the PALS atlas.

·         Open Scene 9: Areal Expansion - Human PALS vs. Macaque F99 (Fig. 4.8).

This shows a map of how the human PALS atlas surface is expanded relative to the macaque atlas. Expansion is low in a few regions (calcarine, central sulcus) and far higher in lateral parietal, lateral temporal, and dorsal prefrontal cortex.

Text Box: Fig. 4.8. Scene 9. Areal expansion map (human PALS vs Core-20-registered macaque F99).

·         Text Box: Fig. 4.7. Scene 8. Macaque sulcal depth, deformed sulcal depth, and PALS average sulcal depth.Select Page Control: Surface Shape, and note that the selected column is labeled: Smoothed Areal Expansion PALS vs F99 (20-LDMK-VE), corrected (Fid vs AvgFid PALS)

In interpreting this map, bear in mind the following points.  (i) The map is logarithmic, base 2.  (ii) The ratio in surface area between each tile on the PALS average fiducial surface and the corresponding tile in the macaque F99 fiducial surface was computed. (iii) The distortions of the PALS average fiducial surface compared to individual fiducial surfaces (Van Essen, 2005a) were taken into account.  (iv) The distortion-compensated expansion map was then smoothed to eliminate noise associated with local irregularities in the registration process, particularly in the immediate vicinity of registration landmarks. 

·         Press the Page Control: Surface Shape: Settings tab, then press the Histogram button to see statistical information about the expansion factor for the population of nodes on the cortical surface.

The average expansion factor is 3.2 log units (~  ), as expected from the ratio of average surface area of human (~900 cm2) vs macaque (~12 cm2). The total range is 5, corresponding to a 32-fold range in expansion factor values. For the 96th percentile, the total range is 3.7, corresponding to about a 30-fold range of expansion.

4.3 Evaluation of registration using fMRI data

·         Text Box: Fig. 4.9.  Scene 10. fMRI activations (object-related): macaque (A), human (B), deformed macaque (C) activation maps.Select Page Control Scene and open Scene 10: Object-related fMRI on flat maps... to view fMRI activations from passive viewing of objects compared to scrambled objects) (Fig. 4.9).

                The main window shows the activation in macaque cortex, viewed on the macaque flat map. Window 2 shows the group-average fMRI activation in human subjects, mapped to the PALS surface by multi-fiducial mapping. Window 3 shows the macaque fMRI deformed to the PALS flat map (using the Core-20-LDMK registration).

The fMRI activations in macaque parietal and inferotemporal cortex (arrows in Fig. 4.9A) are deformed to regions of human cortex (Fig. 4.9C) that do not coincide with the human object-specific activations (Fig. 4.9B).

4.4 Improved registration landmarks.

Text Box: Fig.  4.10. Scene 11. Three fMRI-based landmarks plus the Core-20 landmarks.
.Each choice of registration landmarks represents a hypothesis about presumed homologies between species.  If one assumes that the macaque and human object-related fMRI activations represent homologous regions, this hypothesis can be made explicit by adding appropriate registration landmarks.

·         Open Scene 11: 23-LANDMARKS: Macaque flat map + image of human flat map (Fig. 4.10)

·         Three landmark contours have been added to the Core-20 landmarks.  These are based on interspecies comparisons of object-specific fMRI activations (Denys et al., 2004).

·         Open Scene 12: Macaque sulcal depth Reg2PALS 23-LDMK-VE vs Core-20-LDMK-VE (PALS flat maps)

The two flat maps show the differences between registration of the macaque sulcal depth map to PALS using the 23-landmark constraints (Main Window) and the 20-landmark constraints (Window 2).  The main differences are in the vicinity of the deformed STS and IPS (highlighted nodes; Fig. 4.11).

·         Open Scene 13: Areal expansion 23-LDMK-VE vs LDMK-Core-19-VE (PALS flat maps)

The two flat maps (Fig. 3.20) show the differences in areal expansion associated with the two registrations (23-LDMK-VE in the main window, Core-20-LDMK-VE in Window 2, Fig. 4.12).

       

Fig. 4.11. Scene 12. Deformed macaque sulcal depth:          Figure 4.12 Scene 13. Areal expansion maps 23-LDMK vs. Core-20-LDMK registrations.                                                  23-LDMK vs Core-20-LDMK registrations.            

 

·         Open Scene 14: Object-related fMRI: Registration # by 23-LDMK vs Core-20-LDMK (Fig. 4.13)

 

4.5 Interspecies interpolation – ‘movies’ of human-macaque warping

·         Text Box: Fig. 4.13.  Scene 14. Deformed macaque object-related fMRI:23-LNDMK vs. Core-20-LDMK registrations.Open Scene 15: Registered-mesh macaque fiducial (main window), Colin fiducial (Window 2) – LATERAL to see the macaque fiducial surface and an individual human fiducial surface (Colin), displayed at the same scale (Fig. 4.14A).

·         In the Main Window, select Model: Human.Colin, press Toolbar: L, then Pan so that its location and orientation match that in Window 2.

·         Select Model: RegF99toPALS... in the Main Window.

·         Select Surface: Interpolate Surfaces

·         In the Interpolate Surfaces window, set the First Surface and the Final Surface to RegF99toPALS_LDMK-23-VE....73730.coord, then set Surface 2 to Human.colin.R…..73730.coord.

·         Change Interpolation Steps to 40 (from the default 20).

·         Text Box: Fig. 4.14.  Macaque F99 fiducial and human Colin fiducial surfaces at same scale in lateral (A) and medial (B) views.  Interpolation between the two standard-mesh surfaces generates ‘movies’ of interspecies registration.Move the Interpolate Surfaces Window to the side of the Main Window.

·         Press the Interpolate Surfaces: Apply button to see a ’movie’ that gracefully warps the macaque fiducial surface to the shape of the target human fiducial surface.

Sequences like this can be easily converted to MPEG movies using the File: Record Main Window Image as Movie option (? Add to Part 4?).

·         Open Scene 16: MEDIAL view: Registered-mesh macaque fiducial (main window), Colin fiducial (Window 2) to see medial views of the macaque and human fiducial surfaces (Fig. 4.14B).

·         In the Main Window, select Model: Human.Colin..., press Toolbar: M and Pan so that it matches Window 2.

·         Select Model: RegF99toPALS in the Main Window.

·         In the Interpolate Surfaces window, set the First Surface and the Final Surface to RegF99toPALS_LDMK-23-VE....73730.coord, then set Surface 2 to Human.colin.R…..73730.coord.

·         Change Interpolation Steps to 40 (from the default 20).

·         Press the Interpolate Surfaces: Apply button to see a medial view of the macaque-to-human warping.

Note that mpeg movies of this sequence can be readily generated using the File: Record Main Window Images as Movie option, but the details are not described here.

4.6 Comparing deformed macaque orbitofrontal areas to human orbitofrontal areas.

An interesting comparison is to ascertain the degree to which deformed macaque orbitofrontal areas are in register with human orbitofrontal areas.  These areas were identified by similar architectonic analyses done in the same laboratory, and several of these areas have been used as landmarks to constrain the registration. 

·          Open Scene 17: Orbitofrontal comparison (def FerryEtAl borders, OngurEtAl paint) on zoomed flat, inflated, very inflated (23-LDMK-VE) to see the deformed macaque borders (Ferry et al. 2000) overlaid on the human orbitofrontal painted areas (Ongur et al., 2003).  This registration involved the 23-LDMK-VE registration constraints.

·         Open Scene 18: Orbitofrontal comparison (def FerryEtAl borders, OngurEtAl paint) on LOBAR flat, inflated, very inflated (23-LDMK-VE) to see the same borders and painted areas on a lobar flat map, thereby avoiding the discontinuity of a large frontal cut (Fig. 4.15A).

·         Open Scene 19: Orbitofrontal comparison (def FerryEtAl paint, OngurEtAl borders) on LOBAR flat, inflated, very inflated (23-LDMK-VE) to see the reverse pattern, with human orbitofrontal borders overlaid on the painted deformed macaque areas (Fig. 4.15B).

Overall, there is good agreement between the two schemes in some regions, as indicated by the common coloring of borders and areas.  However, there are definite discrepancies (e.g., macaque area 12xx in red largely overlapping human area 10xx?, plus others…).  Altogether, this suggests that human and macaque orbitofrontal areas are not simply scaled versions of one another (cf. Ongur et al., 2003; Ferry et al., 2000; Van Essen, 2005c for further discussion).

Fig. 4.15. Comparison of humans and deformed macaque orbitofrontal areas, using deformed macaque borders on human painted areas (A) and human borders on deformed macaque painted areas (B).

4.7. Spec files for Routine Analyses.

The following scenes provide various configurations that can be useful  when comparing different partitioning schemes for macaque and human cortex and for a variety of additional analyses of existing data or for new data that you may wish to overlay.

·         Open spec file: Human_Macaque_COMPARISONS.RIGHT.STANDARD-SCENES.73730.spec

·         Open the first scene: Human PALS Flat, Inflated, VeryInflated plus registered macaque data (23-LDMK-VE)

Text Box: Fig. 4.16. Template scene for monkey-human comparisons on PALS surfaces
.This shows template flat, inflated, and very-inflated human atlas maps with PALS average depth as a background (Fig. 4.16).   No macaque-specific data are visible, but many macaque data files registered to PALS are loaded and can be readily viewed by selecting the appropriate paint column, surface shape column, or border type.

·         Open the second scene: REG2PALS-Lewis-VE areas, borders on Human PALS Flat, Inflated, VeryInflated RIGHT (23-LDMK-VE)

This shows the Lewis & Van Essen (2000a) areas (borders plus painted regions) overlaid on the PALS atlas surfaces (Fig. 4.17)

·          Open the third scene: REG2PALS-Lewis-VE areas on Human visuotopic areas, PALS Flat, Inflated, VeryInflated RIGHT (23-LDMK-VE)

This shows the Lewis & Van Essen (2000a) borders overlaid on human visuotopic areas.

·         Text Box: Fig. 4.17. Deformed Lewis & VE (200a) areas on PALS atlasOpen the fourth scene: Orbitofrontal: deformed macaque borders on Human areas, PALS Flat, inflated lateral, medial (RIGHT)

This shows the Ferry et al. (2000) orbitofrontal areal boundaries overlaid on human orbitofrontal areas (Ongur et al., 2003).  Orbitofrontal: deformed macaque areas on Human borders, PALS Flat, inflated lateral, medial (RIGHT)

·         Open the sixth scene: Orbitofrontal: deformed macaque areas on Human borders, PALS Flat, inflated lateral, medial (RIGHT)

This shows the reversed arrangement, with human orbitofrontal areal boundaries (Ongur et al., 2003) overlaid on Ferry et al. (2000) orbitofrontal areas.

 

End of Part 4.


Part 5: Specific/selected analysis procedures

Caret has numerous options for analyzing data in ways that create new files or modify existing ones.  Part 5 illustrates how to carry out a few commonly used major operations.  Additional options are covered in The Caret 5.5 User Guide to Analysis Procedures.

5.1 Mapping fMRI volume data – Average Fiducial and Multi-Fiducial Mapping.

Many fMRI studies are analyzed by registering the MRI volumes from individual subjects to a standard stereotaxic atlas, then carrying out statistical analyses on the volume-averaged group data.  The PALS atlas can be used to view volume-averaged fMRI results on a surface without the biases imposed by an individual subject’s particular convolutions.

§         In a terminal window, change to the CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ subdirectory.

§         Type ls *.HEAD and note that there are two volume fMRI files (BURTON_04_VibroTactile_EARLY_BLIND and BURTON_04_VibroTactile_SIGHTED) ready for mapping onto the PALS atlas.

§         Launch caret5.

5.1.1 Making a project-specific spec file

§         Select the Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.

§         Press Select All, then press Create New Spec...

§         Select the Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file, but don’t press Open.

§         Instead, change the middle part of the name read to PALS_B12.BOTH.Test-Map-fMRI.73730.spec, then press Open

This creates a new spec file menus and also switches the spec file menu to this new version (see label along top).

§         Press the Load Scene(s) button.

5.1.2 Mapping multiple volumes onto both hemisphere surfaces

§         Select Attributes: Map Volume(s) to Surface(s)

§         In the Map Volumes to Surfaces window press Next (accepting the default selection of ‘Metric (Functional) Data’).

§         In the Volumes Selection: Volume Thresholding section, check the box next to Enable Entry of Volume Threshold.

§         In the Volumes Selection: window press Add Volumes from Disk.

§         Select the following two fMRI volumes: BURTON_04_VibroTactile_EARLY_BLIND+orig.HEAD and BURTON_04_VibroTactile_SIGHTED+orig.HEAD and press Open.

§         Enter 3.5 for the positive threshold and -3.5 for the negative threshold for each of the selected volumes.

                  Note: The choice of threshold is up to the investigator, and typically should represent a cutoff for statistically significant voxels.

§         Press Next.

§         Press Map to Spec File with Atlas.

This will map data to your atlas of choice, and enter the resultant metric file(s) into the chosen spec file.

§         In the Atlas Surface Selection window, select Output Spec File: Human.PALS_B12.BOTH.Test-Map-fMRI.73730.spec file. Select Open.

§         Select Mapping Atlas: space: 711-2C, then select Mapping Atlas: Atlas: PALS_B12 Multi-Fid Map LEFT hemisphere.

§         Press OK

Note on target spaces. The available atlas spaces include 711-2B [Colin], 711-2C, SPM2, SPM99, SPM96, SPM95 FLIRT, MRITOTAL, and AFNI versions of stereotaxic space. If, for example, your data are in the afni version of Talairach space (i.e., with ‘+tlrc’ in the file name), then choose Mapping Atlas: AFNI space. If your data are in the Washington University 711-2B space, use Mapping Atlas: 711-2C space (711-2B and 711-2C are essentially equivalent in this context.).  For comments on the differences among these spaces, see http://brainvis.wustl.edu/help/pals_volume_normalization/.  The mapper also can be used to map data from an individual subject from the volume to the surface.

§         Press Map to Spec File with Atlas again, then select the same output spec file as before (...BOTH.Test-Map-fMRI...)

§         Select Mapping: Atlas: Space: 711:2C and Mapping Atlas: PALS_B12 Multi-Fid RIGHT hemisphere

              This will result in both hemispheres being processed concurrently.

§         Then press Next in the Spec File and Surface Section page

§         In the Mutli-Fiducial Mapping Metric Output, leave the default selections: ‘Show Mapping to Average Fiducial Surface’ and Show Average of Mapping to All Multi-Fiducial Cases’ options selected. 

              The other output options are largely self-explanatory and are generally needed only in special circumstances.

§         In the Data File Naming: Data File text box, highlight and delete the default name (map_data_0…..metric) then enter a more informative name: PALS_BURTON_04.LEFT.COMPOSITE.73730.metric, then press SAVE.

§         Highlight the newly entered metric file and copy (-C) just the filename (not the directory)

§         Press the Surface Family pulldown menu and select the second entry (ending in ‘right 711-2C’)

§         Highlight and delete the default file name (map . . .), then paste in the previously copied metric file name (PALS_BURTON_04.LEFT.COMPOSITE.73730.metric)

§         Change ‘LEFT’ to ‘RIGHT’ in the new metric file name.

§