Caret 5 User’s Guide to

Analysis Procedures

John Harwell, Heather A. Drury,

Donna Dierker, and David C. Van Essen

 

Caret Version 5.5

22 September, 2006

 

Copyright 1995-2006 Washington University

Washington University School of Medicine

Department of Anatomy and Neurobiology

St. Louis, Missouri USA 63110

http://brainmap.wustl.edu


Table of Contents

Overview........................................................................................................................................................................... 3

Downloading and installing Caret 5 software................................................................................................................. 3

Additional Source of Help for Caret............................................................................................................................. 3

Obtaining Caret analysis procedures data set............................................................................................................ 3

Starting Caret 5 and Opening a Specification File...................................................................................................... 4

Setting Preferences......................................................................................................................................................... 4

The Mouse....................................................................................................................................................................... 5

Visualizing Surfaces........................................................................................................................................................ 5

Visualizing Volumes........................................................................................................................................................ 5

Surface and Volume Interaction.................................................................................................................................... 6

Using the Display Control Dialog................................................................................................................................. 7

Surface Overlay and Underlay Data Types.................................................................................................................... 7

Viewing Paint and Metric Surface Data.......................................................................................................................... 8

Volume Overlay and Underlay Data Types.................................................................................................................... 8

Viewing Functional Volumes........................................................................................................................................... 9

The Identify Window..................................................................................................................................................... 10

Combined Surface and Volume Viewing...................................................................................................................... 11

Viewing Three Metric (Functional) Data Sets Simultaneously................................................................................ 12

Importing and Exporting Files....................................................................................................................................... 13

Importing FreeSurfer Files into Caret........................................................................................................................... 13

Borders.............................................................................................................................................................................. 15

Drawing an Open Border............................................................................................................................................... 16

Drawing a Closed Border............................................................................................................................................... 16

Surface Region Of Interest Operations........................................................................................................................ 18

Converting a Surface to Volume................................................................................................................................... 20

Capturing Images of the Main Window...................................................................................................................... 21

Creating Movies.............................................................................................................................................................. 21

View Right and Left Hemispheres Simultaneously.................................................................................................... 22

Scenes............................................................................................................................................................................... 23

Command Line Programs................................................................................................................................................ 23

caret_command............................................................................................................................................................... 23

caret_copy_spec.............................................................................................................................................................. 23

caret_edit......................................................................................................................................................................... 23

caret_file_convert............................................................................................................................................................ 23

caret_map_mfri............................................................................................................................................................... 23

caret_metric..................................................................................................................................................................... 23

caret_zip_spec................................................................................................................................................................. 23

 

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.


Overview

Caret 5 is a software application for analyzing, manipulating, and viewing surface and volume models of the cerebral and cerebellar cortex and for displaying experimental data on the surfaces and volumes.

Text Box: Figure 1 - Fiducial Surface, Flat Surface, and Volume with fMRICaret 5.5 (September 2006 release) has many visualization procedures covered in the Caret Tutorial – the Basics (September, 2006), referred to herein as ‘the Basics document’.  The current ‘User’s Guide’ covers a number of  additional analysis options.  It assumes that the user is familiar with Caret 5.5 capabilities covered in ‘the Basics’ document.  Each section contains an explanation of functionality followed by tutorial steps to demonstrate the functionality.  The document can be followed in a linear fashion, or by skipping to topics of particular interest.

As in the Basics document:

Downloading and installing Caret 5 software.

See Appendix 1 of the Basics document (Caret_Tutorial_Basics_Sept06.pdf in the SumsDB Tutorials directory)

Additional Source of Help for Caret

General comment.  This tutorial is an ‘interim adaptation of an older (March 2005) tutorial in which standard-mesh surface representations, the PALS population-based atlas, and scenes were not available. Hence, aspects of this are covered in the ‘old-fashioned’ way.

Obtaining Caret analysis procedures data set

The data set for use with this tutorial is available in “zip” format from SumsDB (http://sumsdb.wustl.edu). Users should follow the link http://sumsdb.wustl.edu/sums/directory.do?id=6594259.  On the SumsDB web page, there is column named name containing the file name: CARET_5.5_USER-GUIDE_ANALYSES.tar

.  To the left of this name in the action column is a download icon.  Select this icon, which will popup a menu, and select download to automatically start downloading the archive (set of files).

After downloading the data set, the archive needs to be uncompressed.  Linux and Macintosh users should run the command unzip CARET_5.5_USER-GUIDE_ANALYSES.tar.  Windows XP users should place the mouse over the downloaded file and press the right mouse button.  From the popup menu, choose Extract All and follow the prompts.  As an alternative, Windows user’s may extract the files by running caret_unzip CARET_5.5_USER-GUIDE_ANALYSES.tar (provided the Caret installation’s “bin” directory is in the user’s PATH environment variable.

Starting Caret 5 and Opening a Specification File

See Section 1.1 of the Basics document if you need help in launching Caret from a Linux, Windows, or Mac OSX platform.

Setting Preferences

(See also Section 1.5.1 of the Basics document)

The preferences dialog is launched by selecting File: Preferences (Caret 5: Preferences on Macintosh).  The preferences dialog allows adjustment of settings that are preserved after Caret 5 is exited.  Some of the available preferences are:

-          Surface Background Color sets the background color of the Main Window and all of the Viewing Windows.  The three values are for the red, green, and blue color components.  The values range from 0 to 255.

-          Surface Foreground Color sets the color used for text occasionally displayed in the main window such as number s for the palette’s color bar when displaying functional data.  If you make the background and foreground colors that same you will not see anything drawn in the foreground color.

-          Light Position is the position of the light that enables the surface to be shaded.

-          Mouse Speed enables the effect of the mouse, such as in surface rotation, to be adjusted.

-          Iterative Update adjusts the frequency with which the surface is updated during some iterative operations such as smoothing.

-          Image Capture provides two selections for the method used to capture images from the Main Window.  The default value is preset based upon the operating system and, in most cases, should not need to be changed.

-          Debug Enabled enables debugging message to be printed when this is selected.  Turning this on may be helpful if you are having a problem with Caret and the messages printed may be included in your bug report.

-          Debug Node A node number for which debugging information is printed when debugging is enabled.

-          Display Lists Enabling display lists may significantly improve the manipulation of the surfaces.  Leave this item on unless error message are printed regarding OpenGL.

-          Speech is available only in Macintosh OSX versions of Caret.  When set to Off, no speech is produced.  When set to Normal, announcements are made during or at the completion of some operations.  In addition, if an error, information, question, or warning dialog is displayed, the type of the dialog is announced.  When Speech is set to Verbose, all Normal announcements are made plus the textual contents of error, information, question, and warning dialogs.

-          Text File Float Precision – This parameter determines the number of digits to the right of a decimal when floating point numbers are written to a Caret text format data files.  This can be an issue when using the “caret_morph” program to perform command line multi-resolution morphing as the results may be different than those obtained by running multi-resolution morphing in Caret 5 immediately after flattening the surface.  For maximum precision, set this value to 24.  Using binary files eliminates the need to set this parameter.

-          File Writing Preference – Determines the format (text or binary) in which Caret 5 data files are written.  When set to “No Preference” a data file is written in the same format as it was read from or text if it is a new file.  The advantage of binary files is that they are much faster to read.  Reading a text data file takes about four times as long as it does to read a binary data file.  Binary data files are written so that they are readable on any computer for which Caret 5 is available.  The command line program “caret_file_convert” may be used to convert Caret 5 data files between text and binary format.

-          Random Seed – Some of the statistical algorithms use the computer’s random number generator.  This allows the user to set the “random seed” for generation of random numbers.

The Mouse

The mouse is used to perform a number of operations in Caret 5.  These operations include adjusting the view of the surface (rotate, scale, and translate), identifying data items, and drawing borders and cuts.  The computer systems on which Caret 5 runs have one, two, or three mouse buttons.  To maintain consistency, most mouse functions are identical across computer systems.  Almost all mouse operations involve using the left (or only) mouse button, sometimes combined with the shift or ctrl (Apple on Macintosh) keys.  Listed in the status bar at the bottom of the Caret 5 main window are the functions of the mouse based upon the current mouse mode.  Caret 5 also has a pop-up menu that is displayed when the user presses the right mouse button (on Macintosh, press the mouse while holding down the control key).  The contents of this menu depend upon what is under the mouse, surface as a border, focus, or surface, at the time the mouse button is pressed.

Visualizing Surfaces

If you are not comfortable with various aspects of viewing surfaces in different configurations and windows using the toolbar, mouse, and menu options, you can spend some time reviewing them here, or else visit the Basics document (Sections 1.1 – 1.10).

  Visualizing Volumes

   (See also Section 1.12 of the Basics document)

Besides displaying surfaces, Caret 5 can also display volumes. 

 

·         In the Main Window, select Model: VOLUME

The default view of the volume sets the viewed slices so that the slices intersecting at the origin are shown.  The origin is commonly set at the Anterior Commissure (AC), however, for some volumes the origin may be set differently. Caret is capable of displaying both orthogonal (right angle or the standard coronal, horizontal, and parasagittal) and oblique (any axis) volume slices.  When viewing a volume you will notice changes in the Toolbar compared to when a surface was displayed.

Toolbar controls for volume visualization:

-          Text Box: Figure 2. Main Window Volume Viewing Horizontal SliceView - Places the mouse in View Mode to that the volume may be translated and zoomed.

-          R – Resets the view of the volume resetting translation and zooming and resets the slices to the default slices (typically the anterior commissure).

-          Slice View Control – Allows selection of viewing a coronal, horizontal, or parasagittal slice, all (coronal, horizontal, and parasagittal) oblique, x-oblique, y-oblique, z-oblique, and oblique all (x, y, and z).


-           

-          Text Box: Figure 3 - Oblique Volume ViewingParasagittal Slice Control

-          Coronal Slice Control

-          Horizontal Slice Control

-          D/C – Pops up the Display Control Dialog.

Surface and Volume Interaction

Text Box: Figure 4 – All Slice Volume ViewingCaret 5 provides the ability to perform surface and volume interactions.  This allows the user to identify a location on a surface and, as a result, the volume slices and crosshair will change to highlight the location in the volume.  Likewise, if a voxel is identified in the volume, the node nearest that voxel will be highlighted on the surface with a green symbol and a large blue cross will briefly appear.


 

Using the Display Control Dialog

(See also Section 1.7 of the Basics document)

 

The Display Control Dialog is used to control the coloring of surfaces and volumes using the loaded data files. At the top of the dialog a control facilitates selection of different control panels for each type of data.  On the most commonly used panel, Overlay/Underlay – Surface, each row has controls for different types of surface attribute data that are used to color the surface.  Some items will be disabled (grayed out) depending upon the data types that are loaded.   On the right half of the dialog are three columns labeled Primary Overlay, Secondary Overlay, and Underlay.  A different data type may be assigned to each of the overlays and the underlay enabling the display of several types of data simultaneously.    The primary overlay takes precedence over the secondary overlay, which takes precedence over the underlay.

In the Main Window, set the viewed brain model to the FIDUCIAL surface.

Surface Overlay and Underlay Data Types

Each of the surface attribute data files is similar to the rows and columns of a spreadsheet with one row for each node and one or more columns of data.  The data types available for coloring a surface are:

-          Text Box: Figure 6- Display Control Dialog Overlay Underlay - Surface PageAreal Estimation is essentially a “fuzzy paint file”.  That is, the boundaries of identified regions are known to be in error and this is reflected in the coloring of the surface near the boundaries between regions.

-          CoCoMac (Collations of Connectivity data on the Macaque Brain) is a database  that combines  the results of many studies of cortical connectivity in the Macaque.  See http://www.mon-kunden.de/cocomac/)  for more information.

-          Metric is simply one or more floating point (real) numbers per surface node that is colored using a palette file.  Typically metric files contain the results of functional neuroimaging studies.

-          Paint contains one or more discrete (integer) values per node that index into a table of names that are typically used to identify regions of the surface.  The names in the table are matched to names in the Area Color File to color the surface nodes.  Columns in the paint file represent partitioning schemes for different cortical areas.

-          Probabilistic Atlas contains partitioning schemes from several subjects.  The surface is colored to show correlation between the different partitioning schemes.

-          RGB assigns red, green, and blue color components to each node.

-          Surface Shape is essentially the same as metric data except that the surface is colored with shades of gray.  Typically surface shape files contain data that represent the shape of the surface such as curvature (folding), or sulcal depth.

-          Topography contains polar angle and eccentricity mappings for each node in the surface.

-          Crossovers show the results of a crossover check (Surface Menu: Measurements: Crossover Check).

-          Sections – If a number is entered in the text box, that section will be highlighted in blue.  If the number is followed by an “X”, every nth section will be highlighted, i.e., a value of “10X” results in every 10th section being highlighted.

-          Edges displays the edges in a surface in blue.  Edges are determined by Surface: Topology: Classify Nodes.

-          Geography Blending requires a column in the paint file named Geography.  Nodes whose geography contains the name “SUL” are darkened to reveal the sulci when other surface node coloring schemes are used.  The Geo Blend factor controls the contrast between gyral and sulcal domains.

   Viewing Paint and Metric Surface Data

   (See also Sections 1.16, 1.18, 1.22 of Basics document)

 

By default, Caret 5 initializes the primary and secondary overlays to “none” and the underlay to the first column in the surface shape file.  If there is no surface shape file, Caret 5 will determine the mean curvature (folding) of the first fiducial or raw surface that was loaded.

·         Set the Main Window so that it displays the FIDUCIAL surface. 

·         Set the Viewing Window 2 so that it displays a FLAT surface. 

·         In the Display Control Dialog, set the Primary Overlay to Paint by selecting the radio button at the intersection of the Paint row with the Primary Overlay column. 

·         If the Paint selection is not Lobes, select Lobes using the control in the Paint row.  The surface is now colored with pastel colors showing the cortex’s lobes. 

·         Notice that the flat surface no longer shows the surface folding, so, set the Underlay to Geo Blend (Geography Blending) making the sulci visible by shading them in a darker color. 

·         Change the Paint selection to Brodmann, which will shade each of the Brodmann areas in a different color.   Notice the abrupt boundaries of each of the Brodmann areas.

·         Change the Primary Overlay to Areal Est (Areal Estimation).  Areal Estimation is similar to Paint but takes into account the fact that the boundaries are not 100% accurate and shades the surface to reflect this inaccuracy.

·         Set the Primary Overlay to Metric and the Underlay to Shape (Surface Shape). 

·         Change the selected Metric to Attention Shifts pop avg using the control in the Metric row. 

·         Press the ? button in the Metric row to display comment information about this functional data.  At the bottom of the comment data is a hyperlink, which, when pressed, displays the abstract of a paper describing the study (UNIX users may need to set the environment variable CARET_WEB_BROWSER or set the web browser using the Preferences Dialog selectable from the File Menu). 

·         Press the Close button on the Comment Editor Dialog.

   Volume Overlay and Underlay Data Types

   (See also Section 1.17 of Basics document)

Several types of volume files may be loaded into Caret 5. Similar to surfaces, several different types of volumes may be displayed simultaneously using two overlays and an underlay. The data types available for coloring a volume are:

-          Anatomy containing a structural MRI.

-          Functional containing functional data such as PET or fMRI (analogous to a surface metric file).

-          Paint whose voxels are indices into a table of names that identify regions of the volume (analogous to a surface data Paint file).

-          RGB containing RGB (red, green, blue) components for each voxel.

-          Segmentation containing voxels that denote a region of interest in the volume.  Segmentation volumes are currently used for volume of interest operations and will be used when SureFit’s segmentation capabilities are added to Caret 5.

·         Using the control at the top of the Display Control Dialog, switch to Overlay/Underlay - Volume.

·         Set the Primary Overlay to Function-View.  Check to see that the selected functional volume is the Corbetta Attention Shift volume. 

·         While still viewing the Attention Shifts pop avg Metric data on the surface, set the Viewing Window so that it shows VOLUME

·         Text Box: Figure 7– Display Control Dialog Overlay/Underlay - Volume PageClick on the peak activations (yellow and orange) on the surface to see the VOLUME view to jump to the corresponding location in the volume (and vice versa).  The activations may be easier to see on the inflated surface.

·         To see how the surface and volume are aligned, press the Show Surface Outline check box in the Miscellaneous frame of the Overlay/Underlay – Volume panel on the Display Control Dialog.

    Viewing Functional Volumes

    (See also Section 1.22 of the Basics document)

 

Functional volumes are colored using the parameters on the Metric panel of the Display Control Dialog.  If a metric file is loaded, it is possible that a functional volume may not be colored correctly.  This will occur if the selected metric was not mapped from the selected functional volume.  If the Color Mapping is set to Auto Scale and the selected metric and the selected volume are different measurements, the effect on the functional volume’s coloring may be even more conspicuous.  While this may seem inconvenient or prone to error, it results in voxels and surface nodes having the same value being colored identically.

·         Set the Viewing Window to show the FLAT surface. 

·         Set the Main Window to the FIDUCIAL surface.

·         Set the Display Control Dialog back to Overlay/Underlay Surface

·         Set the Primary Overlay to Metric.

·         Change the Metric selection to view – VISUAL MOTION Lewis et al.

·         Press the ? button to view information about the functional data including a URL linked to the data’s publication.

·         Switch the Display Control Dialog from Overlay/Underlay – Surface to the Metric panel which allows greater control over the display of Metric (Functional) data. 

·         Press the Selection tab to list all of the metric data that is loaded. 

·         Press the radio button in the Thresh column to threshold – VISUAL MOTION.  Leave the View column set to view – VISUAL MOTION

·         Press the Settings tab. 

·         In the Threshold frame, set the Positive value to 0.2, so that no positive values less than 0.2 are displayed, and press the Apply button at the dialog. 

·         In the Display Mode frame, press the radio button next to Positive so that only positive values are displayed.

·         Press the checkbox next to Display Color Bar in the Palette frame.

·         Set the Display Control Dialog to Overlay/Underlay – Surface.

·         Near the bottom of the Display Control Dialog is a row named Lighting EnabledUncheck the check box in the Primary Overlay Column and notice that the functional data no longer has lighting applied to it, and thus reflecting its true color.

·         Set the Secondary Overlay to Paint and the Underlay to Geo Blend while leaving the Primary Overlay set to Metric

·         Change the selected Paint to Visuotopic to see identified visual areas under and around the functional data (this is best viewed on the flat map).

   The Identify Window

   (See also Section 1.18.1 of the Basics document)

 

The Identify Window may be used to better understand the relationship between the functional data and the visuotopic areas. In the Identify Window, information about the identified point on the surface is presented.   Buttons in the toolbar of the Identify Window are used to filter the information that is printed in the Identify Window.  Placing the mouse over the buttons will display a tooltip describing the filtering function of the button.

Identify Window Toolbar Buttons:

-          CID – Removes all node identify symbols (green squares) on all of the surfaces.

-          Clear – Erases the contents of the Identify Dialog.

-          Copy – Copies text highlighted by mouse dragging to the clipboard for pasting into other programs.

-          B – Allows/disallows display of border identification.

-          C – Allows/disallows display of cell identification.

-          F – Allows/disallows display of foci identification.

-          V – Allows/disallows display of voxel identification.

-          C – Allows/disallows display of node coordinate.

-          X – Allows/disallows display of node section.

-          L – Allows/disallows display of node latitude/longitude.

-          P – Allows/disallows display of node paint.

-          p – Allows/disallows display of probabilistic atlas.

-          R – Allows/disallows display of node RGB paint.

-          M – Allows/disallows display of node metric.

-          S – Allows/disallows display of node probabilistic atlas.

-          A – Allows/disallows display of node areal estimation.

-          Text Box: Figure 8 - Identification DialogT – Allows/disallows display of node topography.

-          All-N – Turns all of the node specific allow/disallow buttons on or off.

-          SID – Toggles between allowing and not allowing green ID symbols to be displayed on the surfaced when an ID Node operation is performed.

-          The number on the far right is the number of digits to the right of the decimal point that will be shown when numeric data is displayed.

·         Click the left mouse button over one the functional activation that is also over a red visuotopic area.

·         Press the Clear button to remove any existing information. 

·         Press the All button to turn off all of the surface data and then press the P button to display Paint information. 

·         Click the left mouse over the activation that is overlayed on the red paint area (If you click over an existing green identification symbol it will be turned off, so, if this is the case, click the left mouse button again).  Displayed in the Identify Dialog will be all of the information from the Paint file for the identified node.  The 4th column will identify the visuotopic area as Visuotopic.MTplus.

   Combined Surface and Volume Viewing

    (See also Section 1.12 of the Basics document)

 

This viewing mode shows volume slices in each axis along with the surface.

·         Using the Display Control Dialog, set the panel to Overlay/Underlay – Surface

·         Set the Primary Overlay to Metric, the Secondary Overlay to No Coloring, and the Underlay to Shape

·         Set the Metric to Attention Shifts Pop Avg

·         Set the Display Control Dialog to the Metric panel. 

·         Text Box: Figure 9 - Main Window Surface and Volume ViewingSet the Display Mode to Both and set the Positive Threshold to 0.0.  Press the Apply Button.

·         Set the Display Control Dialog panel to Overlay/Underlay – Volume

·         Set the Primary Overlay to Functional, the Secondary Overlay to No Coloring, and the Underlay to Anatomy

·         In the Main Window, use the Model Selection Control to select SURFACE VOLUME.

·         Press the Toolbar:L button to see a lateral view. 

·         In the Toolbar, change the rotation axis to XY (the combo box to the left of the D/C button). 

·         While holding down the left mouse button, move the mouse slowly from right to left and down slightly so that all three slices and surface are visible. 

·         On the Display Control Dialog, set the panel to Surface and Volume.

·         Press the check box next to Show Primary Overlay in the Volume Overlays frame so that the functional data is displayed on the volume slices.  You should see an image like that in Figure 9.  The volume slices can be turned off and the display slices numbers adjusted in the Anatomy Volume frame.

·         Text Box: Figure 10 - Main Window Surface and Volume Viewing Functional VoxelsClick the check box next to Show Surface in the Surface frame so that the surface is not displayed.

·         Press the check box next to Show Volume Cloud in the Functional Volume frame to show all of the functional voxels in their 3D locations. 

·         Use the mouse to rotate the surface (while holding down the left button) or the standard view buttons in the Toolbar to change the view.  

·         Turn the surface display back on by pressing the check box next to Show Surface to visualize the relationship of the voxels to the surface similar to that in Figure 10.

Viewing Three Metric (Functional) Data Sets Simultaneously

At times, it may be desirable to view several metric columns simultaneously.  This is accomplished by converting the three metric columns into an RGB paint file where one metric column is assigned to each of the color components (red, green, and blue). 

There are three sections in the Metrics to RGB Paint Dialog (Figure 11.).  The RGB Paint section allows the user to choose an existing column in the RGB Paint File or to create a new column.  In addition, a comment may be entered for the column.

The Metric Selection section allows the user to choose up to three metric data columns for conversion to RGB Paint.  Both negative and positive values may be stored in an RGB Paint file column, however, the display of positive and negative values is mutually exclusive.  As a result, both the Neg Max and Pos Max values are mapped to the full intensity of the color component.  When a metric column is selected in the Metrics to RGB Paint Dialog, Neg Max is initialized to the most negative value in the metric column and Pos Max is initialized to the most positive value in the metric column.  Considering just the positive metric values, any metric value greater than or equal to Pos Max is mapped to full color intensity.  A metric value of zero is mapped to zero color intensity (black).  Values between zero and Pos Max are linearly interpolated to an intensity between black and the full color intensity.  Using a very small Pos Max, say 0.001, would result in all of the metric data being mapped to the full color intensity with no darker shades of that color.

The Threshold Selection section allows each of the metric columns selected in the Metric Selection section to be thresholded.  This is optional and the thresholding column for a color component may be different than the corresponding color component in the Metric Selection section.  By default, the Positive and Negative thresholding values are zero which results in no thresholding.  If the positive metric value for the selected threshold color component is less than the Positive thresholding value, the metric value is mapped to zero intensity (black).

·         Set the Main Window surface to FLAT using the Model Selection Control

·         Select Attributes:Metric: Convert Metric to RGB Paint

·         In the RGB Paint frame, leave the column set to Create New Column and set the name of the column to “Functional”. 

·         In the Metric Selection frame, set Red to Attention Shift Pop Avg, Green to Eye Movements Pop Avg, and Blue to view – VISUAL MOTION. 

·         In the Threshold Selection frame set Red to Attention Shift Pop Avg, Green to Eye Movements Pop Avg, and Blue to threshold – VISUAL MOTION.  Set the Red and Green Positive thresholds to 3.5 and the Blue Positive Threshold to 0.1.  This will eliminate metric values that are not of statistical significance.

·         Text Box: Figure 11 – Metrics to RGB Paint DialogThe dialog should appear like that in Figure 11.  Press the Apply button followed by the Close button. 

·         On the Display Control Dialog’s Overlay/Underlay – Surface panel, set the Primary Overlay to RGB, the Secondary Overlay to No Coloring, and the Underlay to Shape

·         Set the RGB selection to Functional on the Overlay/Underlay – Surface panel of the Display Control Dialog.

·         Switch to the RGB Paint panel on the Display Control Dialog

·         Turn off the Blue channel by unchecking its check box. 

Areas of the surface that are red indicate activity during the Attention Shift task but not during the Eye Movement task.  Likewise, areas of the surface that are green indicate activity during the Eye Movement task but not during the Attention Shift task.  Areas in yellow indicate activity during both the Attention Shift and Eye Movement tasks. 

·         Press the ? button in the Red row to show comment information that was automatically transferred from the Metric file. 

·         Turn off the Red channel by unchecking its check box. 

·         Enable the Blue channel by checking its check box, setting its Threshold to 0.04, and pressing the Apply Button.  Areas colored in cyan indicate activity during both the Eye Movement and Visual Motion tasks.

Importing and Exporting Files

Caret 5 supports the importation of non-Caret 5 data files and the export to non-Caret 5 data files.  To see a list of file types supported for import and export, select either File: Import Data File or File: Export Data File.  The types of files supported are listed in the File Type control.  Caret 5 does support importing surfaces from programs such as Brain Voyager and Free Surfer.

Importing FreeSurfer Files into Caret.

 

Caret provides options not only for importing FreeSurfer files (and other file types), but also for additional processing that provide useful ‘value-added’ surface representations.  Most notably, landmark-based surface-based registration to the PALS atlas can be done without repeating the segmentation and initial surface reconstruction processes if these have already been done in FreeSurfer.

 

In brief, these capabilities include:

- Menu options as well as command-line options to import/convert FreeSurfer geometry [and other] files to Caret format.

- Menu options as well as command-line options to generate mid-thickness (layer 4) coordinate files (by averaging the smoothwm and pial FreeSurfer files).

- Command-line generation of sulcal depth, folding, and ‘geography’ files that are conceptually similar to the FreeSurfer ‘curv’ and ‘sulc’ files but have some advantages.

 

§         Launch Caret from a directory that contains FreeSurfer surfaces (a right hemisphere rh.* in the example here).

§         Select Toolbar: File: Import File: FreeSurfer Surface Ascii Surface File: rh.smoothwm.asc

                   Import Selections:  Check the Right Hemisphere box and leave Import Topology and Import Coordinates checked.

·         Select File name: rh.smoothwm.asc

·         Press Open

·         Select File: Save Data File

         File type: Topology Files

         Save As Type: Closed

         File name: Human.<Case>.R.CLOSED.<NodeNumber>.topo

                         Including the number of nodes in file names of files belonging to a common ‘surface family’ is a useful way to quickly ascertain compatibility across files.

·         Press Save

Would you like to create a spec file?  Yes.

         Species: Human

         Subject: <CASE>

         Hemisphere: Right

         Space: Other

         Category: INDIVIDUAL

·         Press OK

Accept default filename for spec file by pressing OK.

 

·         Select File: Save Data File

         File type: Coordinate Files

         File name: Human.<CASE>.R.SMOOTHWM.<NodeNumber>.coord

         Save As Type: Fiducial

         Hemisphere: Right

         Coord Frame: Native

         Orientation: Left Posterior Inferior

·         Press Save

Several additional FreeSurfer files that are useful to import have already been pre-imported in order to save  you time.

            Tips.  Several tips to bear in mind when importing multiple FreeSurfer Files into Caret.

                  (i)   When importing multiple surface files from the same hemisphere, you only have to save the topology file once

                  (ii)  When saving multiple Caret files, you can save time by selecting one file name, then just changing the relevant part of it (e.g., File name: Select Human.<CASE>.R.SMOOTHWM.<NodeNumber>.coord, but backspace over SMOOTHWM and type PIAL, so resulting filename reads "Human.<CASE>.R.PIAL.<NodeNumber>.coord")

                  (iii) When importing curvature files as surface shape Caret currently filters only for ‘*, curve, asc’ files. This glitch will be fixed soon. In the meantime. . . .

                  (iv) You cannot import files having a different number of nodes (e.g., an ‘rh.occip.patch’ file when rh.smoothwm is already loaded).

                  (v)  For a command-line utility that streamlines this process, see http://brainvis.wustl.edu/pipemail/caret_users/2006-February/000686.html

 

Generating a mid-thickness fiducial surface by averaging gray/white and pial surfaces

 

The imported FreeSurfer data files have been assigned to a Caret spec file.

·    Select File: Open Spec File: Human.<CASE>.RIGHT.<NodeNumber>.spec.

·    Press Select all files and press Load.

·   Select Surface: Create Average Coordinate File and select Add

·   Select both Human.<CASE>.R.PIAL.<NodeNumber>.coord and Human.<CASE>.R.SMOOTHWM.<NodeNumber>.coord.

·   Press Open

·     Change Output Coordinate File from “average.coord” to “Human.<CASE>.R.FIDUCIAL-MidThickness.<NodeNumber>.coord”

·   Deselect: Create Sample Standard deviation

·    Press Apply, then press OK on pop-up that says it’s been created, then press Close.

·    Select File: Open Data File

File type: Coordinate Files

File name: Human.<CASE>.R.FIDUCIAL_MidThickness.<NodeNumber>.coord and press Open.

·    Select File: Save Data File

File type: Coordinate Files

Save As Type: Fiducial

Hemisphere: Right

Coord Frame: Native

Orientation: Left Posterior Inferior

File name: Human.<CASE>.R.FIDUCIAL_MidThickness.<NodeNumber>.coord

·    Press Save, then Yes to Overwrite Existing File

Borders

Borders are used to delineate regions of a surface.  There are two types of borders, open and closed.  Open borders are simply a set of connected line segments.  An example of using an open border is during flattening of a full hemisphere in which open borders denote where cuts in the surface should be made.  Closed borders are similar to open borders but the last point in the border connects to the first point in the border, thereby enclosing a region of the surface.  During surface flattening a closed border is used to enclose the medial wall so that it may be removed.  Closed borders are also used in region of interest operations described later in this document.  Display of borders is controlled using the Display Control Dialog. The Main border sub-panel allows the display of borders, as a whole, to be turned on or off and control over the drawing style of borders (points or lines).  The Name sub-panel permits the display control of borders with identical names and the Color sub-panel permits display control of borders by the assigned color.  Operations on borders are accessible through the Layers: Borders menu.

Borders are stored in two types of files, Border Files and Border Projection Files.  A border file stores borders as sets of three-dimensional points that are for use with a specific surface coordinate file.  Each border file is assigned a type (fiducial, spherical, flat, etc) just like a coordinate file.  When a border file is loaded (say a flat border file), it is displayed only on surface of a matching type (in this case a flat surface).  Border Projection files store each border point in relation to three nodes in the surface and Barycentric Coordinates within those three nodes.  This allows a border projection file to be displayed on any type of surface (fiducial, flat, etc) for an individual.

Figure 12- Brodmann Borders on Fiducial and Flat Surfaces

·         If no borders are loaded, load border color and border projection files as described in the Opening Data Files section of this document. 

·         View several of the surfaces using the Model Selection Control and notice that since a border projection file was loaded, the borders appear on all of the surfaces. 

·         Set the Main Window so that it displays the FLAT surface. 

·         Change the panel on the Display Control Dialog to Border and press the Color tab. 

·         Press the All Off button to disable the display of all border colors. 

·         Press the LAT and LONG check boxes to display latitude and longitude borders (latitude and longitude is a spherical coordinate system often used for navigating about the earth). 

·         Disable the display of LAT and LONG and select the Brodmann check box to see borders that enclose the Brodmann areas. 

·         To see which areas a Brodmann border delimits, click the left mouse button over a border to perform an ID border operation.  In most cases, two borders will be listed in the Identify Dialog since there are actually two borders, one superimposed on the other, each enclosing the respective Brodmann area. 

Drawing an Open Border

·         Text Box: Figure 13 – Open Border Along Central SulcusSelect  Layers:Borders: Delete All Borders and press the Yes button in the Confirmation Dialog.  This will eliminate the numbers borders currently loaded.

·         Select Layers:Borders: Draw Borders

·         Drag the Draw Borders Dialog off of the Main Window

·         In the Draw Borders Dialog, enter Border1 for the Name, set the Type to Open and press the Apply button. 

·         After pressing the Apply button, the Create Border Color Dialog pops up allowing you to set the color for the border.  Set the color to cyan by dragging the Red slider to the far left, the Green and Blue sliders to the far right, and press the OK button. 

·         Move the mouse over the Main Window to the bottom of the central sulcus.  While holding down the left mouse button, drag the mouse to the top of the central sulcus and release the left mouse button. 

·         Now, while holding down the Shift Key, click the left mouse to tell Caret that you are done drawing the border and notice that its color changes from red to cyan as show in Figure 13.

 

Drawing a Closed Border

·         Go back to the Draw Borders Dialog and change the name of the border to Border2, change the Type of the border to Closed, and press the Apply button. 

·         In the Create Border Color Dialog set the color to magenta by dragging the Green slider to the far left, the Red and Blue sliders to the far right, and then press the OK button. 

·         Move the mouse to the bottom of the central sulcus. 

·         Text Box: Figure 14- Closed Border Around Central SulcusWhile holding down the left mouse button, draw the mouse in a clockwise orientation around the perimeter of the central sulcus. 

·         When the mouse returns to a point near the starting point of the border, release the left mouse button, hold down the shift key and click the left mouse button to complete the border.  Notice that since this is a closed border, additional border points between the end and start of the border are added as shown in Figure 14.

 

The next border will enclose the post-central sulcus.  However, we do not want the border to overlap with the border we just drew around the central sulcus so we will the use the augment feature while drawing this border. 

·         In the Draw Borders Dialog, change the name to Border3, leave the Type set to Closed, and press the Apply button. 

·         In the Create Border Color dialog, change the color to yellow by dragging the Blue slider to the far left, the Red and Green sliders to the far right, and press the OK button. 

·         Move the mouse to the left side of the post-central sulcus.  While holding down the left mouse button start drawing the border in a clockwise direction. 

·         When the mouse gets near the border that was drawn around the central sulcus, release the left mouse button. 

·         Hold down the CTRL key (Macintosh users should hold down the Apply key) and click the left mouse button while over a point on the border that encloses the central sulcus.  Notice that the mouse pointer changes to a small cross.  While still holding down the CTRL (Apple) key, click the left mouse near the bottom left of the central sulcus border.  Notice that the mouse returns to a pointer shape. 

·         Continue drawing the border by dragging the mouse with the left mouse button held down to near the starting point of the border. 

·         Release the left mouse button, hold down the shift key, and click the left mouse button to close the border as shown in Figure 15.

 

When drawing a closed border, the paint attributes of the nodes within the border may be assigned.

·         Text Box: Figure 15. Closed Border Around Post-Central SulcusIn the Draw Border Dialog, change the Name to Border4.

·         Set the Type set to Closed.

·         In the Closed Border Paint Assignment frame, check the Assign Paint Identifiers to Nodes Within Border check box.

·         Set the Paint Column to Create New Column and enter Areas in the text box on the right.

·         Press the Apply button.

·         In the Create Border Color Dialog, choose a color for Border4 and press the OK button.

·         In the Set Area Color Dialog, press the Define Area Color button.

·         In the Create Area Color Dialog, choose a color for the nodes that is different than the color just set for the border and press the OK button.

·         Use the mouse to draw a border by as described previously.

·         Using the Display Control Dialog, switch to the Overlay/Underlay – Surface panel.

·         Set the Primary Overlay to Paint and set the selected Paint to Areas.  You should now see the nodes within Border4 set to the color that you defined.

·         Press the Close button on the Draw Borders Dialog.

Text Box: Figure 16.  Border Drawing an Assign Nodes ExampleNow that you have drawn some borders, you would like to see these borders on the fiducial surface.  However, it is difficult to draw borders on a three-dimensional surface.  So, the solution is to project the flat borders. 

·         While viewing the FLAT surface and the borders that you just drew in the Main Window, select Layers:Borders: Project Borders. 

·         Choose Nearest Tile in the Projection Method Dialog that pops up and press the OK button.

·         Change the surface in the Main Window to the FIDUCIAL surface and set to a lateral view (Toolbar: L) to see the borders.

As an exercise, draw borders and assign nodes reproducing those show in Figure 16.

Surface Region Of Interest Operations

Region of interest operations allow measurements to be made of and operations performed on a subset of the surface.  There are three steps involved in performing a region of interest task in Caret 5.  First, the surface nodes of interest must be chosen.  Secondly, the surface for the operation must be chosen.  Lastly, the operation and its parameters must be set.

Substantial flexibility is provided for node selection.  Nodes may be selected by their paint attributes, metric (functional) attributes, and their inclusion within a border.  When selecting nodes by their paint attributes, the paint attribute may be selected from a list or a node may be clicked with the mouse and the node’s paint attribute will be obtained.  Two methods are available for selecting nodes by their metric attributes.  Both allow the nodes to be filtered by upper and lower thresholds.  The first method selects all nodes that are within the upper and lower thresholds.  The second method allows a node to be selected with the mouse and then all nodes connected to the selected node whose metric values fall within the threshold are selected.  When selecting nodes within a border, the border may be selected by clicking it with the mouse or by selecting the name of the border.  An additional control is provided to select nodes in disjoint or intersecting regions.

Several operations may be performed on the selected nodes with the Region Of Interest Dialog.  These operations include assigning paint attributes to nodes, creating a volume of interest (segmentation volume), disconnecting nodes (breaking the links), performing geodesic distance measurements for a specific node, smoothing selected nodes, and obtaining a statistical report.

Example of statistical report on a paint region:

·         Set the Main Window so that it displays the FLAT surface.

·         Using the Display Control Dialog’s Overlay/Underlay Surface panel set the Primary Overlay to Paint, the Secondary Overlay to No Coloring, and the Underlay to Shape.  Set the Paint to Lobes

·         If borders are displayed, remove them using the Display Control Dialog’s Border panel.

·         Select Region of Interest Operations from the Surface menu and drag the Surface Region of Interest Dialog the right of the Main Window.

·         In the Region of Interest Node Selection frame, set the Selection Method to Nodes With Paint

·         Set the Category to LobesPress the Select Name From List button and, in the Paint Name Selection Dialog that pops up, select LOBE.FRONTAL and press the OK button.  Press the Select Nodes button and you should see the frontal lobe turn green (selected nodes are shown in green).

·         In the Operation Surface and Topology frame, set the Surface to FIDUCIAL and the Topology to CUT.

·         In the Operate on Selected Nodes frame, set the Operation to Statistical Report on Selected Nodes.  An option, Tab Separate Report (for import to spreadsheet), is provided which will separate the columns in the report with tabs so that the report can be imported into a spreadsheet such as Excel.  Press the Create Report button, and, within a short time, the dialog will switch to the report output.

At the top of the report is information about the query and the number of nodes that were selected along with the surface area of the entire surface and the selected region.  In the metric section of the report, statistics for the query nodes are provided for each column in the metric file.  The same is true for the surface shape file.  In the paint section, information is provided showing the surface area and percentage of total surface area that have the paint attribute and are within the query region.  The report may be saved to a file using the Save To File pushbutton or cleared with the Clear button.

Converting ROIs to Paint node attributes and a Segmentation Volume

·         Using the Display Control Dialog set the Primary Overlay to Metric, the Secondary Overlay to No Coloring, and the Underlay to Shape.  Set the selected Metric to Attn Shifts, Pop Avg.

·         Press the Query tab to return to the query page on the Surface Region of Interest Dialog.

·         In the Region of Interest Node Selection, press the Deselect Nodes button to clear the currently selected nodes. 

·         Set the Selection Method to Nodes With MetricSet Threshold Low to 3.0 and High to 50000.0.  Select the Nodes Within Threshold Connected to Node Selected With Mouse

·         Click the mouse over the Activation that is in parietal cortex (Point A in Figure 17).  Setting the Secondary Overlay to Paint – Lobes may help. 

·         Press the Select Nodes button.  You should see the activated area turn green, indicating that the nodes are selected. 

·         Below the Select Nodes button, change the control from Normal Selection to Or Selection (Union). 

·         Click the mouse over the activation that is in the posterior part of the frontal cortex (Point B in Figure 17) and press the Select Nodes pushbutton.  You should now see the two disjoint activations in green indicating that they are selected as shown in Figure 18.

·         In the Operation Surface and Topology frame, check to see the Surface is FIDUCIAL and that the Topology is CUT.

 

·         Text Box: Figure 17.  Functional Regions of InterestIn the Operate on Selected Nodes frame, set the Operation to Assign Paint Attributes to Selected Nodes.  Set the Paint Column to Create New Column and in the text box on the right, which contains the name for the new column, change it to “Activations”.  Set the Paint Name to “hotspot”.  Press the Assign Paint button.  In the Create Area Color Dialog that pops up, set the color to magenta by dragging the Green slider to 0, leave both the Red and Blue sliders at 255, and press OK button.

·         In the Operate on Selected Nodes frame, set the Operation to Create Volume ROI from Selected NodesPress the Create Volume Query From Displayed Query Nodes button.  In the Create Region Of Interest Volume Dialog’s Surface Selection frame, set the surface to FIDUCIAL, Thickness to 1.0, Thickness Step to 0.5, and the Offset to zeros.  In the Volume Selection frame change the Space to WU 711-2B 111Press the OK button.  This may take a minute or two to complete.

·         Press the Deselect Nodes button in the Region of Interest Node Selection frame.

·         Set the Main Window to display the FIDUCIAL surface.

·         Text Box: Figure 18.  Functional Regions Selected to ROI OperatonOn the Display Control Dialog’s Overlay/Underlay – Surface panel, set the Primary Overlay to Paint with Activations as the selected Paint and you should see two magenta regions representing the regions selected. 

·         Set the Main Window to display VOLUME.

·         On the Display Control Dialog’s Overlay/Underlay – Volume panel, set the Primary Overlay to Segmentation, the Secondary Overlay to No Coloring, and the Underlay to Anatomy.

·         Use the Toolbar to select a horizontal view.  Set the selected slices to 131, 119,115.  You should see two red regions (segmentation volume voxels are always drawn in red) representing the activated areas. 

·         Set the Secondary Overlay to Functional and set the Functional Volume to Attention Shifts Pop Avg to see the regions of interest in relation to the functional data.

Viewing Geodesic distances:

·         Change the Main Window to the FLAT surface. 

·         Using the Display Control Dialog’s Overlay/Underlay – Surface panel, set the Primary Overlay to No Coloring, the Secondary Overlay to No Coloring, and the Underlay to Shape.

·         In the Region of Interest Node Selection frame, set the Selection Method to Entire Surface.

·         Below the Select Nodes button, set the type of selection to Normal Selection.

·         Press the Select Nodes button.

·         In the Operation Surface and Topology frame, set the Surface to FIDUCIAL and the Topology to CLOSED.  It is important to use the closed topology to avoid inaccurate distances due to cuts.

·         In the Operate on Selected Nodes frame, set the Operation to Geodesic DistancePress the Choose Node With Mouse button and click the left mouse button inside the Sylvian Fissure. 

·         Set the Metric Column to Create New Column and enter the name “Geo Dist”.

·         Leave the Geodesic set to Create New Column.

·         Press the Determine Geodesic Distances button.  It may take several minutes to determine the geodesic distances.

·         Press the Deselect Nodes button in the Region of Interest Node Selection frame.

·         Set the Primary Overlay to Metric.  Set the Metric to Geo Dist.

·         Change the Display Control Dialog to the Metric panel.  Set the Palette to Geodesic+.  With this palette, red represents nearby regions and yellow regions that are further away.

·         Change the Display Control Dialog to the Geodesic panel.  Select the check boxes next to Enable Geodesic Path for Identified Nodes and Show Root Node.

·         Click the mouse on different surface locations.  The shortest path along the surface from the node used to calculate the geodesic to the identified node will by displayed in cyan.  This may function best on the fiducial or inflated surfaces.

Converting a Surface to Volume

Caret 5 allows volumes to be created by intersecting a fiducial surface with a newly created empty volume.  Three different types of volumes may be created.  Paint Volumes are created from a single column in a currently loaded Paint File.  Functional Volumes are created from a single column in a currently loaded Metric File.  RGB volumes are created using the current node coloring.

 

·         Select Attributes:Paint:Convert Paint Column to Paint Volume.

·         In the Copy Surface Paint Column to Paint Volume Dialog set the Surface Selection to FIDUCIAL

·         Set the Volume Selection Space to 711-2B-111 since the tutorial surface is in 711-2B 111 space.  This will automatically set the parameters that specify the volume dimensions, voxel size, and origin.

·         Set the Paint to Brodmann.

·         Press the OK button to create the Paint Volume.  This may take 5 to 10 minutes.

·         Set the Main Window to VOLUME.

·         Text Box: Figure 19.  Brodmann Paint Volume Over AnatomyUsing the Display Control Dialog’s Overlay/Underlay Volume panel, set the Underlay Volume to Anatomy, the Primary Overlay to Paint and the Secondary Overlay to No Coloring.

·         Scroll through the slices to view the Paint Volume overlayed on the Anatomy Volume.

·         Since this volume took a while to create, you may want to save the volume.  Select File:Save Data File to launch the Save Data File Dialog.

·         Set the File Type to Volume File – NIFTI (*.nii *.nii.gz), Volume File - WUNIL (*.ifh) or Volume File – AFNI (*.HEAD) since these are the only formats that currently support Paint Volumes.

·         In the Save Parameters frame, set the Volume Type to Paint.

·         Enter a name for the file in the File Name text box.

·         Press the Save button to save the file.  The file will be saved and the file information will automatically added to the spec file.

 

Capturing Images of the Main Window

The contents of the Main Window may be saved to an image file.  Caret 5 has two methods that it uses for capturing the Main Window image.  On some computer systems, one of the methods is preferable to the other.  The image capture method is selected on the Preferences Dialog available from the File Menu (on the Caret 5 menu on Macintoshes).   If the quality of the image is not as desired, try the other image capture method.  In addition, at times, a ghost image of the Save Image File dialog may appear in the image.  Alleviate this by dragging the Save Image File dialog off the Main Window prior to saving the image.

·         Select File Menu: Capture Image of Main Window menu item to pop up the Capture Main Window Image Dialog

·         In the Capture Type section, select Select Part of Graphics Area With Mouse.

·         In the Image Destination section, select Save to File.  If you are on a Mac or Windows computer with a word processor such as Microsoft Word, also select the Copy to Clipboard check box.

·         Verify the Name is set to capture.jpg.

·         In the main window, place the mouse outside of the surface, hold down the left mouse button, drag the mouse so that a red box encloses the surface, and then release the left mouse button.

·         Press the Capture push button.  A file in the current directory named capture.jpg will have been created.

·         If you selected Copy to Clipboard, start your word processor and select Paste from the word processor’s Edit menu.  You should see the image you just captured pasted into your document.

Creating Movies

Caret 5 has the capability to successively capture images from the Main Window and save them to an MPEG movie file.  When recording, temporary image files are written to the current directory and assembled into an MPEG movie file when the user presses the Create Movie button on the Recording Dialog.  Two methods of recording, Automatic and Manual, are available.  Automatic recording captures an image from the Main Window each time the graphics in the Main Window are updated.  Manual recording captures an image from the Main Window each time the Capture button on the Recording Dialog is pressed.  Prior to recording any images, the width and height of the movie image may be set.  When the movie width and height of a specific size is desired, it is best to start Caret 5 with the “-xy” option and specify the desired width and height (ie: “Caret 5  -xy  352  240”).  Since MPEG movies typically play at a rate of 30 frames per second, the Recording Dialog allows each captured image to be repeated an adjustable number of times.  Once the user has created a movie the Recording Dialog’s Reset button will clear any existing temporary images allowing the user to start a new movie.

·         Switch to the Overlay/Underlay Surface panel on the Display Control Dialog.  Set both the Primary Overlay and the Secondary Overlay to No Coloring and the Underlay to Shape.

·         Set the Main Window to the INFLATED surface.

·         Place the surface in a lateral view using the Toolbar:L button.

·         Set the Main Window to the FIDUCIAL surface press the Toolbar:L button to place the fiducial surface into a lateral view.

·         Select Surface:Interpolate Surfaces to launch the Interpolate Surfaces Dialog and move the dialog so that it does not obscure the Main Window

·         In the Interpolate Surfaces Dialog, set the Interpolation Steps to 10.  Set the Topology File to CUT (…CartStd..)Set the First Surface to FIDUCIAL, Surface 2 to INFLATED, and Surface 3 to FLAT (…CartStd)Set Surface 4 and Final Surface to None

·         Select File:Record As MPEG to launch the Recording Dialog and move the dialog so that it does not obscure the Main Window.

·         Set Record Each Image to 5 times.

·         Select the radio button labeled Automatic so that images from the Main Window are automatically captured.

·         Return to the Interpolate Surfaces Dialog and press the Apply button.  The surfaces will be interpolated and recorded which will take several minutes.

·         On the Recording Dialog, select the Manual radio button so that recording is off.

·         Press the Create Movie button to convert the temporary images into an MPEG movie file named “output.mpg”.

·         View “output.mpg”.  Windows and Macintosh users may double click the file to view it.  Unix users may use the program “mpeg_play” included in the Caret 5 distribution to view the movie.

·         Press the Reset button on the Recording Dialog to erase the temporary images.

View Right and Left Hemispheres Simultaneously

While Caret was originally designed to view a single hemisphere at a time, Caret is now able to load multiple spec files.  When multiple spec files are loaded, all of the surface and volumes are available in the Model Selection Control on the Main and Viewing Windows.  All operations and the Display Control window operate on the Spec File containing the surface displayed in the Main Window.

·         Use the Display Control Dialog’s Overlay/Underlay – Surface panel to set the Primary Overlay to Metric, the Secondary Overlay to No Coloring, and the Underlay to Shape.

·         Set the selected Metric to Attention Shifts Pop Avg.

·         Set the selected Shape to Folding (mean curvature).

·         Choose File:Open Spec File.  In the Open Spec File Dialog, navigate up one directory and then down into the Left_HEM directory.  Choose the only spec file.

·         In the Spec File Dialog press the Select All button followed by the Load button to load all files.  In the New Spec Dialog, choose Keep Loaded Spec so that the right hemisphere remains in memory.

·         Use the Display Control Dialog’s Overlay/Underlay – Surface panel to set the Primary Overlay to Metric, the Secondary Overlay to No Coloring, and the Underlay to Shape.

·         Set the selected Metric to Attention Shifts Pop Avg.

·         Text Box: Figure 20  Viewing Right and Left HemispheresUse the Main Window’s Model Selection control to select All Fiducial Surfaces.  You should now see both the right and left hemispheres displayed.

·         Press the View button in the Main Window ToolbarHold down the left mouse button and drag the mouse to rotate the fiducial surfaces.

 

    Scenes

(See also Section 1.11 of the Basics document)

 

Scenes provide a method for saving “the state” of Caret.  By “state” we mean all loaded files, the models displayed in the Main and Viewing Windows, and all Display Control settings.  When making figures for a paper or presentation it is often helpful to create a scene, so, if a change needs to be made to the figure, the state of Caret at the time the original image was captured can be quickly reproduced.

Creating a scene:

·         Open up at least one Viewing Window from the Window Menu.

·         Set the overlays and underlay for the surfaces and/or volumes as desired.

·         Switch to the Scene Page on the Display Control Window.

·         Press the Append New Scene button and enter a name for the scene you are creating.

·         Select Save Data File from the File Menu.

·         In the Save Data File Dialog, set the File Type to Scene Files and enter a name for the scene file.  Press the Save button to save the file.

·         Quit Caret by selecting Exit from the File Menu (use Quit Caret 5 from the Caret 5 Menu on Macintoshes).

·         Restart Caret 5 and reopen the Spec File you were just viewing (it should be the first item on the File->Open Recent Spec File Menu.

·         Press the Load Scenes button near the bottom of the Spec File Dialog.

·         In the Display Control Window’s Scene Page, double-click the name of the scene you created in one of the previous steps.  It may take a minute or two to load the files and the state of Caret at the time you created the scene will be restored.

Command Line Programs

Each of the command-line programs requires parameters for successful usage.  To see a list of the parameters and other help information, run the program with the parameter “-help”.

    caret_command

caret_command is a command-line program for performing operations on surfaces and volumes on the command line.  Run the program with the argument “-help” to see a list of the program’s capabilities.  The Script Builder, available from the Window Menu, provides a user interface for building a script using caret_command.

   caret_copy_spec

caret_copy_spec is a command-line program for copying a spec file.  The data files may be copied depending upon the parameters provided to the program.

   caret_edit

caret_edit is a simple text editor that is able to edit all text files regardless of the type of newline characters.  For your information, Macintosh OSX, Microsoft Windows, and UNIX all use different characters to indicate a newline in a text file.  Thanks Bill Gates, Steve Jobs, and some unknown pocket-protector-wearing UNIX dork.  The text editor may also be launched from Caret’s Window menu.

   caret_file_convert

caret_file_convert is a command-line program that converts Caret 5 data files between text and binary formats.  It can convert a single file or many files.

   caret_map_mfri

caret_map_fmri is a command-line program for mapping functional volume data to a surface.

   caret_metric

caret_metric is a command-line program that performs clustering and smoothing of metric files.

   caret_zip_spec

caret_zip_spec is a command line program for zipping a spec file and its data files into a “.zip” file.