Caret 5 Changes

(26 Nov 2007) Changed version to 5.512.
(19 Nov 2007) Add "-volume-create", "-volume-create-in-stereotaxic-space", and "-surfaces-to-segmentation-volume-mask" to caret_command.
(19 Nov 2007) On Save Data File Dialog, hide prob atlas volume selection combobox so that all prob atlas volumes are saved to a file.
(19 Nov 2007) Add StudyMetaDataLinks to Areal Estimation, Prob Atlas Surface File, and Prob Atlas Volume File.
(19 Nov 2007) Default the File Open Dialog to the current directory.
(19 Nov 2007) When a paint is identified, do not show linked study metadata if the paint name begins with a question mark (?). In addition do the same for metric values of zero.
(19 Nov 2007) On Foci Attribute Assignment Dialog, allow deselection of a hemisphere for assignment.
(19 Nov 2007) Fixed display of foci geography attribute in identification dialog.
(16 Nov 2007) Add "-color-file-create-missing-colors" which adds random colors to a color file for some data files when the data file name does not have a matching color.
(14 Nov 2007) Fixed bug with Surface Region of Interest Dialog, which enabled the display of ROI nodes when displayed but failed to check recheck the Show Selected Nodes checkbox.
(14 Nov 2007) Fixed bug that prevented the Surface Menu->View->Switch to User View menu from being loaded with saved user views.
(14 Nov 2007) Fixed bug that resulted in the a WuQFileDialog always asking the user to confirm overwriting a file even if the file did not exist.
(13 Nov 2007) Add import of MDPlot and Neurolucida files to caret_command -file-convert.
(13 Nov 2007) Add mouse mode control to main window toolbar.
(12 Nov 2007) Fix -cog option for caret_command -surface-place-foci-at-limits.
(12 Nov 2007) Add "Contour Information" to Layers->Contours menu to show the geometric and section extent of the contours loaded in Caret.
(09 Nov 2007) Add a smoothing option to "caret_command -surface-border-merge".
(08 Nov 2007) caret_command -show-scene: Fixed problem with transformations being incorrect for windows other than the main window. This was due to the drawing always drawing in the "main window" and using its transformation instead of the transformation for the viewing window.
(07 Nov 2007) Add multiple file writing preferences.
(02 Nov 2007) Fix Display Control crash that occurred when a paint column was selected on the Paint page prior to creation of the Overlay/Underlay Surface page.
(02 Nov 2007) Fix crash when choosing a directory on the Copy Spec File Dialog.
(02 Nov 2007) Fix very slow update of Display Control Dialog's Shape Selection Page when loading additional surface shape file data.
(02 Nov 2007) Fix reading of "Nearest Node" option on Border Projection Dialog.
(02 Nov 2007) Fix directory only mode on WuQFileDialog.
(01 Nov 2007) Reformat preferences dialog.
(01 Nov 2007) Remove speech generation.
(31 Oct 2007) Add "-file-read-time" to caret_command to time the reading of a spec file's data files and also some caret data files such as coordinate, border projection, foci projection, metric, spec, surface shape, and topology files.
(31 Oct 2007) Modify file filters used on Open Data File Dialog so that shape files can be opened as metric files and metric files can be opened as shape files.
(30 Oct 2007) Remove QT3 compatibility flag from qmake files so that Caret no longer uses QT3 Support library.
(30 Oct 2007) Added multi-threaded spec file reading which can reduce the time to read a spec file by 30% or more. To enable multi-threaded spec file reading, go to the Preferences Dialog (on the File Menu for Linux and Windows and Caret menu on Mac OSX) and set the File Reading Threads to at least 2. A good setting may be 2 times the number of cores per CPU times the number of CPUs.
(24 Oct 2007) Add Study Data Type and Study Data Format to Study Metadata.
(23 Oct 2007) Fix appending of study meta data files so that provenance data is not lost. When saving a study metadata file, prompt for provenance data if there are any studies without provenance data.
(23 Oct 2007) Fix Layers-Border option on Display Control's Overlay/Underlay Surface page.
(22 Oct 2007) Add an option, "-allow-start-end-the-same", to "caret_command -surface-border-draw-geodesic" that allows the output border to contain only a single link.
(22 Oct 2007) Added support for 64-bit signed and unsigned integer data types for NIFTI volume files.
(19 Oct 2007) Replace QFileDialog with WuQFileDialog, an improved File Dialog.
(19 Oct 2007) Fixed problems on Open Data File Dialog involving a copy data file error and selection of file type when using the "any" file filter.
(19 Oct 2007) Fixed problems on Save Data File Dialog involving incorrect file extension (.border) added to a border projection file and not initializing the filter to the previous file filter.
(19 Oct 2007) Fixed Sums Dialog's upload file dialog so that it initializes to the current directory.
(19 Oct 2007) Fixed prepending of column prefixes when deforming node data files.
(19 Oct 2007) Fixed update of column names on Shape Math Dialog when the column names are changed on the Display Control Dialog.
(17 Oct 2007) Add support for multiple Study Metadata Links.
(12 Oct 2007) Add a command that finds duplicate studies in StudyMetaDataFile's to caret_command.
(09 Oct 2007) Add Open Inventor as one of the surface conversion output formats for caret_command's "-file-convert".
(08 Oct 2007) Combine Open Data File, Import File, and Open Image File Dialogs into a single dialog using a new and improved file dialog. When opening files, multiple files may be selected.
(08 Oct 2007) Combine Save Data File, Export File, and Save Image File Dialogs into a single dialog using a new and improved file dialog.
(05 Oct 2007) caret_command updates: (1) add "-deformation-map-create" to create a deformation map file from two spherical coordinate files; (2) add conversion of caret shape file column to a free surfer curvature file.
(01 Oct 2007) Fixed bug that failed to display the Area attribute on the Cell/Foci report dialog.
(01 Oct 2007) Added "Attribute Assignment" to the Layers->Foci menu that is used to assign the Area and Geography attributes of Foci.
(28 Sep 2007) Fixed a bug that sometimes resulted in a node attribute file (e.g. metric) having a blank column shown as selected on the Display Control even though there is data loaded.
(28 Sep 2007) Fixed problem with unicode characters in strings returned by PubMed.
(20 Sep 2007) Fixed cell density to metric operation crash that occurred if the metric file contained one or more columns.
(18 Sep 2007) Consolidate volume to surface metric and paint mappers into a single mapper.
(18 Sep 2007) Fixed bug, was using maximum voxel neighbors in strongest voxel neighbors algorithm for volume to surface metric mapping.
(17 Sep 2007) Add backward and forward push buttons for page selection.
(17 Sep 2007) Added a variable input command to caret scripting.
(13 Sep 2007) Added Provenance to StudyMetaData.
(12 Sep 2007) Add "Generate Colors for Paints Without Colors" to the Attribute Paint Menu. When selected, this will generate a random color for any paint names that do not have a matching color with the exact same name.
(12 Sep 2007) Add new caret script builder to the Window Menu.
(07 Sep 2007) Fixed display of missing toolbar volume controls when a volume in the 2nd or later brain set was selected for display.
(04 Sep 2007) Change version to 5.511.
(31 Aug 2007) Completed rewrite of "caret_command". "caret_command" now includes the functionality of the programs "caret_file_convert", "caret_copy_spec", "caret_zip_spec", "caret_metric", and "caret_map_fmri". As a result, these programs have been eliminated. Since "caret_command" has been rewritten, the Script Builder Window, available from the Window Menu, has also been eliminated since it is incompatible. In place of it, for now, is "Caret Command Executor", which provides a user-interface for executing all of caret_command's operations. Since all of the metric/shape statistical operations are in "caret_command", and Caret Command Executor provides an interface to them, the Attributes Menu->Metric and Shape statistical operations menu has been eliminated.
(27 Aug 2007) Do not limit the size of foci. If being drawn as OpenGL points do not allow the size to exceed the maximum OpenGL allowed size.
(27 Aug 2007) Add "Strongest Voxel" algorithm for mapping functional volumes to surfaces. For each node, its value is the value of the voxel that is furthest from zero in the local neighborhood.
(23 Aug 2007) Allow cell/foci report dialog to function with both left and right hemispheres.
(10 Aug 2007) When "Update Focus PubMed ID if Focus Name Matches Study" no longer clears the study link when the PubMed ID is not equal to the Project ID.
(31 July 2007) Fixed reading of gifti data arrays that had base64 encoding. Using "const QByteArray ba = text.toAscii(); and const char* textChars = ba.constData();" instead of "const char* textChars = text.toAscii().constData();" fixes the problem.
(27 July 2007) Allow multiple spec files to be selected on the Open Spec File Dialog. Multiple spec files are selected on the dialog by using the CTRL or SHIFT keys and the mouse to select files.
(24 July 2007) When caret is started with "-loadspec spec-file-name" allow the entry of multiple spec files so that multiple spec files my be loaded simultaneously.
(19 July 2007) In Caret file name generation, ignore and no longer use the date in the file name.
(17 July 2007) Add buttons on Surface Region of Interest Dialog for dilating and eroding the selected nodes.
(17 July 2007) Modify automatic linear border drawing to generate an error message if the starting and ending nodes in the border are not connected in the region of interest.
(16 July 2007) Fixed bug so that the color file symbol is properly handled when appending a color file.
(13 July 2007) Add buttons on the Surface Region of Interest Dialog for saving or loading the current node selection.
(06 July 2007) Fixed abort that occurred when creating a new spec file on the spec file dialog.
(05 July 2007) Display study information when a vocabulary entry with a link to study metadata is identified.
(05 July 2007) Correct reading/writing of study metadata links for vocabulary files.
(03 July 2007) At the beginning of surface flattening, check the surface for topological errors (handles).
(29 June 2007) If subject/species/hem not provided by spec file, guess at their values by examining coord and topo file names.
(29 June 2007) Add "-paint-composite" to caret_command.
(22 June 2007) Add a full width half maximum algorithm to metric smoothing. This algorithm smooths until the FWHM is achieved or the maximum number of iterations is reached. The FWHM estimation is based upon formula 2 of the Hagler et. al. article from NeuroImage 33 (2006) 1093-1103.
(20 June 2007) Add a "1.0 - value" operation to volume and metric math operations. The intended use is convert P-Values to "Q-Values". If the users wants to threshold, say less than 0.05, it cannot be done in Caret since caret thresholds "above" values. So, using this operation will allow the user to threshold greater than 0.95.
(19 June 2007) Remove all metric smoothing options except average neighbors from the MetricFile. All algorithms remain in BrainModelSurfaceMetricSmoothing.
(19 June 2007) Add multi-fiducial mapping of paint volumes to surfaces. These options include mapping to the PALS atlas' individual cases, mapping to the average fiducial surface, and in place of average to all cases a most commonly mapped ID for each node.
(19 June 2007) Fixed problem with paint "?" not properly enabled on Display Control's Overlay/Underlay Surface page.
(18 June 2007) When creating a new Study, have user enter the PubMed ID if it is available. If the PubMed ID exists in another study, do not allow the user to create a study using the same PubMed ID.
(18 June 2007) Add provenance (submitter/originator) to Study Meta Data File.
(18 June 2007) Fixed parsing of caret data file names that contained "LR" for the structure.
(15 June 2007) Fixed reading of binary format latitude longitude files.
(14 June 2007) Add "-surface-to-cerebral-hull" to caret_command for generating a cerebral hull volume from a fiducial surface.
(13 June 2007) Add selection of nodes within a latitude/longitude range on the Surface Region of Interest Dialog.
(13 June 2007) Fix volume handle finder handle selection so that it uses stereotaxic coordinates which will work when the underlay volume is a different dimension than the segmentation volume.
(12 June 2007 Add -metric-or-shape-stat-kruskal-wallis to caret_command which performs a Kruskal-Walllis (non-parameteric one-way ANOVA).
(12 June 2007) Increase number of surface outlines shown over volume slices and move the controls from Display Control's Volume Settings page to a new page, Volume Surface Outline.
(12 June 2007) Rebuild QWT libraries due to new QT libraries installed on 08 June.
(11 June 2007) Added a method to the foci projection file that eliminates all foci not in a list of specified indices. This will be used by WebCaret.
(11 June 2007) Changed the following caret_command operations so that they only the name prefix is specified for all output files: "-metric-or-shape-stat-paired-t-test", "-metric-or-shape-stat-one-sample-t-test", "-metric-or-shape-stat-interhemispheric-clusters", "-metric-or-shape-stat-anova-one-way", "-metric-or-shape-stat-two-sample-t-test", "-metric-or-shape-stat-coord-diff".
(11 June 2007) Changed to version 5.510.
(11 June 2007) Fixed cell/and foci reports so that they appear on top of the main window. They were, for some reason, appearing behind the main window.
(08 June 2007) Switch to QT version 4.3.0. Gulp.

Release Caret 5.51 (07 June 2007)

(07 June 2007) Changed version to 5.51.
(06 June 2007) Added "-metric-or-shape-set-column-name" to caret_comand which sets the name of a column.
(06 June 2007) Added "-metric-or-shape-file-info" to caret_comand which prints names and min/max values for all columns.
(06 June 2007) Added "-metric-or-shape-set-column-to-value" to caret_comand which sets all values in a column to a scalar value.
(06 June 2007) Added "-metric-or-shape-create" to caret_comand which creates a metric or shape file with specified number of nodes and columns.
(06 June 2007) Added "-metric-or-shape-correlation-map" to caret_comand which creates a correlation map between two metric/shape files.
(05 June 2007) Added a page to www.wikipedia.org for CARET.
(04 June 2007) Added keyboard commands for panning an zooming contours.
(30 May 2007) Modified algorithm that creates borders around clusters so that it now creates borders around small clusters which it did not do in the past. In addition, there is now an option to automatically project the new borders and borders are automatically displayed.
(29 May 2007) Add Surface ROI option that creates a border from an ROI that represent the fundus of a sulcus or crown of a gyrus.
(24 May 2007) Fixed bug that borders were not displayed if they were first enabled using the pop-up menu.
(24 May 2007) Add option to Draw Borders Dialog that automatically projects a border immediately after the border is drawn.
(22 May 2007) Add -surface-roi-coord-report" to caret_command.
(18 May 2007) Add ability to read free surfer patch files which had their format changed in free surfer version 3.0.5.
(17 May 2007) Add "-volume-histogram" to caret_command which prints a histogram of the input volume to the terminal window.
(17 May 2007) Add "-volume-scale-percent-min-max-255" to caret_command which rescales voxel values excluding percentages of the minimum and maximum values.
(17 May 2007) Add "-volume-anatomy-peaks" to caret_command which prints estimates of intensity values for CSF, gray, and white matter.
(09 May 2007) When cropping a volume, save the cropping parameters to the parameters file.
(09 May 2007) Save gray and white peaks to the parameters file when segmenting (it previously did this only for the GUI, not command line).
(07 May 2007) List the values of the estimated CSF, Gray, and White peaks on the SureFit segmentation dialog.
(07 May 2007) When reading a Neurolucida file, use "SID" attribute of a contour's <point> as the section number.
(04 May 2007) Remove use of vtkDecimateCaret and use vtkDecimatePro instead.
(03 May 2007) Fixed problem with ID node by number (Surface->Identify menu item) not placing green ID symbols on surface.
(01 May 2007) At start of surface flattening algorithm, enable the display of borders needed due to 26 April change.
(30 April 2007) Add "Smooth" button to SureFit segmentation dialog to smooth the histogram and help find gray/white peaks.
(30 April 2007) Improved consistency of volumes so that crosshairs are at the center of a voxel.
(27 April 2007) Correct problem with foci name selections not being saved to a scene.
(26 April 2007) Default the display of borders OFF.
(25 April 2007) Throw exception if reading a comma separated value file is read and it is missing the "csvf-section-end" tag at the end of the last data section.
(25 April 2007) Fixed crash with View Current Files that occurred if no surfaces were loaded.
(24 April 2007) Make improvements in algortithm that estimates the gray and white matter peaks in an anatomy volume.
(23 April 2007) For statistical cluster finding algorithms, generate a region of interest statistical report for each input/shape file.
(20 April 2007) For structure names allow a single character (L) in addition to the full name (Left).
(20 April 2007) When reading a foci file in CSV format, if the structure is not specified, allow the sign of the X-coordinate to imply the structure (minus implies left, positive implies right).
(19 April 2007) Add left-to-left and right-to-right coloring selections for paint and RGB paint.
(19 April 2007) Add check to see if studies from a meta-analysis already exist when working with Study Metadata.
(19 April 2007) When importing data from a meta-analysis file, allow appending or replacement of existing study metadata.
(17 April 2007) Modify surface information reports so that the surface extent is only for connected nodes.
(17 April 2007) Add option "-vc" to caret_file_convert to convert between volume file formats.
(17 April 2007) Change version to 5.503.
(17 April 2007) Add button to color selection dialogs that allows selection of commonly named colors as defined by the world wide web consortium.
(16 April 2007) Added import of MicroBrightfield's Neurolucida XML files that contain contours and markers.
(12 April 2007) Add a page to SureFit Segmentation Dialog that allows the user to set the type of volume files that the segmentation process will write.
(10 April 2007) Added Bias Correction of Anatomical Volumes. The algorithm was taken from AFNI's program 3dUniformize.
(10 April 2007) Added ID filtering of study meta-analysis information on Identify Window.
(09 April 2007) Add new meta-analysis file which contains one meta-analysis study and a list of the studies contained in the meta-analysis.
(06 April 2007) When adding studies contained meta-analysis, make retrieval of data from PubMed optional.
(06 April 2007) Fix retrieval of Medical Subject Heading data when retrieving Study Information from PubMed.
(06 April 2007) Add a "link" button next to PubMed ID in study editor to show the web page for the study.
(06 April 2007) Show meta-analysis info for a study in the Identify Window.
(06 April 2007) Add ability to delete a group of studies by name on the Study Metadata Editor dialog.
(06 April 2007) Fix read of foci x-coord from a comma separated value file.
(06 April 2007) When study metadata editor dialog is launched and there are no studies, create an empty study so that the dialog is properly sized.
(05 April 2007) Added option on SureFit Segmentation Dialog to generate topologically correct surfaces. This option is off by default. If turned on, a dialog informs users about issues and limitation of this option.
(05 April 2007) When generating a surface and maximum polygons is selected, do not perform any polygon decimation. Previously, if maximum polygons was selected, there was some polygon decimation performed if it could be done with very minimal or not change in the shape of the surface.
(04 April 2007) Fix naming of surface shape files produced by SureFit segmentation method so that the file name contains the number of nodes.
(04 April 2007) Add range of values to data type labels on volume rescale dialog.
(04 April 2007) Add -surface-information and -surface-topology-disconnect-paint-nodes to caret_command.
(03 April 2007) Add a PubMed ID to each Caret file. This ID is entered on the File Menu->Save Data File Dialog.
(02 April 2007) Add a Link button next to the DOI/URL on the Study Metadata Editor. When pressed, it will use the DOI/URL to show the article in a web browser.
(02 April 2007) Add Meta-Analysis to Study Meta Data.
(02 April 2007) Save cell/foci highlighting to scene..
(29 Mar 2007) For Thesholding an Anatomical Volume into a Segmentation Volume, an upper threshold was added, the thresholds are now floats, and allowed to have a floating point values.
(28 Mar 2007) Correct lighting problem with export to VRML files.
(28 Mar 2007) Correct iterations problem with Paired T-Test.
(26 Mar 2007) Enable reading of NIFTI volumes that are stored in an analyze hdr/img file pair.
(26 Mar 2007) Add option to pop-up menu to project the border under the mouse.
(23 Mar 2007) Changed reading of Caret data files in Comma Separated Value File format so that the column names are case insensitive.
(22 Mar 2007) Added -volume-segment-mask-creation, which creates a volume mask from a group of volumes, and -volume-mask-volume, which applies a mask volume to a volume file, to caret_command.
(22 Mar 2007) Added "Correct Fiducial Surface Topology (Remove Handles)" to the Surface-Topology menu. This operation will remove all topologial errors (handles) in the main window fiducial surface. It does this by discarding nodes around handles and retessellating the surface. While the resulting surface is topologically correct it is not necessarily anatomically correct.
(22 Mar 2007) When drawing 3D borders, allow the mouse to rotate the surface if the ALT key is depressed. This should help with drawing flattening and registration borders as it will allow the borders to be drawn on 3D (inflated, fiducial) surfaces instead of the flat map and the compressed medial wall surface.
(22 Mar 2007) Add selection of nodes that are crossovers to surface region of interest dialog.
(21 Mar 2007) Add "-surface-topology-neighbors" which generates a list of neighbors for each node in a topology file.
(20 Mar 2007) Fixed problem that occurred on some Linux workstations with the Recording Dialog. On some Linux workstations the function that reports if a file is writable always returns unwritable.
(19 Mar 2007) Add "Update Focus' PubMed ID if Focus Name Matches Study Name" which updates the PubMed ID in the focus' study metadata link if the focus name is the same as the name of a study.
(19 Mar 2007) Add a "Fetch All PMIDs" button on the Study Metadata Editor Dialog. This will update all studies with valid PubMed IDs with data retrieved from www.pubmed.gov.
(16 Mar 2007) When retrieving PubMed Info from the PubMed website, append year, volume, and pages to journal name.
(16 Mar 2007) Add Name and MESH (Medical Subject Headings) to Study Metadata. Remove URL and combined it with DOI since DOI should always go to the correct document.
(15 Mar 2007) Implemented left-on-left, right-on-right coloring option for surface probabilistic atlas.
(14 Mar 2007) Added "Create Interpolated Borders" to the Layers->Borders Menu. This allows the user to create new borders that are interpolated between two selected borders.
(13 Mar 2007) Add a "Fetch" button in the PubMed ID row on the Study Metadata Editor Dialog. When pressed, it grabs the currently entered PubMed ID and queries the PubMed database for title, author, citation, DOI, and abstract and places the results into the currently edited study.
(12 Mar 2007) Fixed problem with foci disappearing when old study data was moved from the foci file to the study metadata file.
(12 Mar 2007) Implemented the addition of a study metadata link for volume files.
(12 Mar 2007) Modify caret_command's two-sample T-Test to have an option of using pooled or unpooled variance. Previously it always did unpooled variance.
(12 Mar 2007) Add "-volume-resize" to caret_command.
(12 Mar 2007) Speed up shuffling of metric columns.
(09 Mar 2007) Fix option on Volume Attributes Editor and Volume Creation dialog for setting the attributes (dimension, spacing, and origin) of a volume.
(07 Mar 2007) For use with permuted metric/shape surface statistics, add a metric file that shows the clusters. The metric file contains two columns, the statistic and (1 - p-value). Use (1- p-value) to threshold the clusters. A new palette "plus_minus" was also added to assist with cluster display.
(07 Mar 2007) Link to Study Metadata Dialog should now be properly initialized when there is an existing link.
(07 Mar 2007) Add information to the project cells/foci dialog that informs user that the sign of the cell/focus is used to determine the associated hemisphere.
(06 Mar 2007) Add "Edit" buttons on spherical deformation dialog that allow editing of the individual and atlas borders. This allows the user to view the borders in a border file, change the names of borders, and/or delete borders.
(02 Mar 2007) Add one-way ANOVA to caret_command. Using two input files, comparing the results of a one-way ANOVA with a two-sample T-Test with pooled variance results in the exact same clusters and the F-Statistics equal to the square of the T-Statistic.
(02 Mar 2007) Eliminated print statement "unknown paint file tag: tag-version" message printed when reading a paint file.
(01 Mar 2007) For foci identification in identify dialog and filtering selection on the identify dialog change "Size" to "Extent".
(01 Mar 2007) Fixed selection of a study on the link to study metadata dialog. This is a QT issue as the signal cellChanged() was no longer emitted so the signal was changed to cellClicked().
(28 Feb 2007) Add "-metric-or-shape-copy-columns-to-new-file" to caret_command. This new command creates a new metric file from column copied from an existing metric file.
(28 Feb 2007) Add metric/shape in group difference, which computes the difference between all possible column combinations, to caret_command. Use the "-metric-or-shape-in-group-diff" option.
(27 Feb 2007) Fix use of optional inner and outer boundaries for surface to volume conversion run with caret_command.
(27 Feb 2007) Add buttons to Study Metadata Editor Dialog that allows selection of studies by name or title.
(27 Feb 2007) When deforming a coordinate file, preserve structure, surface type, etc.
(27 Feb 2007) Add entries on deformation and apply deformation map dialogs to set the node data file deformed column name prefix.
(27 Feb 2007) On apply deformation map dialog, add "*.atlas.paint" to atlas file filter.
(26 Feb 2007) Fixed scrolling of volume slice spin boxes when holding down the mouse button.
(26 Feb 2007) Fixed reading of NIFTI volume that required rotation to become an LPI orientation.
(26 Feb 2007) Add "Bring All to Front" and "Stack Windows" to the Window Menu. "Bring All to Front", available on Mac OSX only, places Caret's windows on top of windows from any other applications. "Stack Window" places all open dialogs/windows over the main window with a small offset.
(23 Feb 2007) Add filtering for all remaining study metadata items.
(23 Feb 2007) When displaying a scene, assign colors to borders, cells, and foci.
(22 Feb 2007) Add filtering for study table data on Identify Dialog.
(22 Feb 2007) Add option on Display Control's Foci Page, "Show Foci Pasted Onto 3D Surfaces" which "pastes" foci onto all 3D surfaces to help expose subcortical foci.
(22 Feb 2007) Correct Foci Color Key when foci are colored by class name.
(21 Feb 2007) When loading files through the spec file dialog and if there are foci (or foci projection) files selected and there are study metadata files but no study metadata files are selected, warn the user. Also, list study metadata files when the foci filter button is selected on the Spec File Dialog.
(21 Feb 2007) When the name on a Foci Color Key is clicked, try to find the corresponding study and display the study metadata in the Identify Dialog.
(21 Feb 2007) Automatically add a subheader when a new table is created on the Study Metadata Editor Dialog.
(20 Feb 2007) Add filtering of study information on the Identify Dialog.
(20 Feb 2007) Add filtering of foci information on the Identify Dialog.
(20 Feb 2007) Fixed uploading of files to SuMS Database. This problem was a result of a bug that was supposed to have been fixed in QT 4.2.2 (See 15 Feb 2007) but was not actually fixed.
(15 Feb 2007) When reading cell/foci files and cell/foci projection files, check for an invalid structure for a cell/focus. If the structure is "invalid" set the structure to "right" if the X-coordinate is greater than zero or set the structure to "left" if the X-coordinate is less than zero.
(15 Feb 2007) Some cell/foci files were not having their structure read correctly but it seems to now be fixed as a result of updating QT to QT 4.2.2. This problems was found when unit testing of foci rendering failed.
(15 Feb 2007) Added unit testing comparison for cell & foci files.
(14 Feb 2007) Updated QT to QT 4.2.2 since it is supposed to contain fixes to bugs that I had reported. Unfortunately, not all the bugs they claim to have fixed are corrected and they have added new bugs such as a Q3FileDialog that is too large to fit on the screen.
(14 Feb 2007) Fixed crash that occurred when the current node coloring was used to create a new rgb paint column.
(12 Feb 2007) Corrected number of non-twin comparisons performed in caret_command's -metric-or-shape-twin-comparison.
(09 Feb 2007) Add options on the foci sub pages to display foci without a class assignment, foci without a color assignment, foci without a link to a study with keywords, and foci without a link to a study table subheader.
(09 Feb 2007) Change "Color" tab on D/C Foci page to "Name" since foci colors are almost always the names of foci.
(09 Feb 2007) Add option to assign the class name to all displayed foci.
(09 Feb 2007) Add option on D/C's Foci Main page to color foci by focus name or by focus class name.
(08 Feb 2007) Add display control of foci based upon the linked study's keywords and table sub header names.
(07 Feb 2007) Correct projection of foci to PALS atlas that broke as a result of adding the new Study Metadata File.
(02 Feb 2007) Fix cleanup paint names when there are multiples of an identical name.
(02 Feb 2007) Add deformation of cell/foci projection files.
(02 Feb 2007) Move some stuff from the MathUtilities class to the caret_statistics library.
(01 Feb 2007) Add a new file, TextFile, for simpler reading and writing of text files and comparison of text files.
(01 Feb 2006) Enable metric/shape files to be read and written as comma separated value files. Unfortunately, Microsoft Excel (prior to Excel 2007) limits the number of rows to 65536. OpenOffice Calc is also limited to 65536 rows.
(31 Jan 2007) Fixed normalize distribution in a metric file. Modified normalization algorithm so that it works with a small number of values.
(30 Jan 2007) Correct deformation of Foci files.
(29 Jan 2007) Fixed deformation of probabilistic atlas files (result of node attribute to gifti conversion).
(29 Jan 2007) Fixed reading of StudyMetaData file's that contained StudyMetaDataTableSubHeader elements. StudyMetaDataTableSubHeader was replaced with StudyMetaDataSubHeader when SubHeaders were added to pages.
(29 Jan 2007) Corrected problem with provenance being updated for all studies when a StudyMetaDataFile was both read and saved. The modification status was triggered when tables and figures were read and added to studies when the file was read.
(29 Jan 2007) Fixed writing of Comma Separated Value File that resulted in elements being enclosed in double quotes when they did not need to be enclosed in double quotes.
(26 Jan 2007) Add new implementation of Volume Region of Interest Operations which adds a new "wizard" dialog, additional voxel selection options, display of selected voxels, and additional operations on selected voxels.
(23 Jan 2007) Fixed P-Value generation for Levene's Test and Metric T-Test, a result of 19 Jan change.
(22 Jan 2007) Add "-metric-or-shape-twin-comparison" to caret_command for use with twin subject comparisons.
(19 Jan 2007) Rewrite and simplify some of the statistical code.
(19 Jan 2007) Slow mouse speed for panning of contours in view and alignment modes.
(18 Jan 2007) Add generation of Root Mean Square (RMS) for metric and shape files.
(18 Jan 2007) Reorganize the basic statistics and move it to caret_common/StatisticUtilities.h/cxx.
(17 Jan 2007) Add item to Layers->Contours Menu to resample all contours.
(17 Jan 2007) Enable Transformation Matrix Editor to apply a matrix to main window contours and contour cells.
(16 Jan 2007) Print a count of the number of points in each contour when reading a contour file. This is used to find contours with an excessive number of points.
(16 Jan 2007) Corrected identification text for voxels which was mistakenly show the identification data more than once.
(16 Jan 2007) The data type for study metadata table number, subheader number, figure number, and page number were changed from integer to string since they may contain non-numeric characters.
(16 Jan 2007) Fixed scene bug that caused identified node symbols to not be displayed. This was a result of new identification code from 02 Jan 2007.
(12 Jan 2007) Add "Page Reference" to Study Metadata File and update Study Metadata editor.
(11 Jan 2007) Rewrote the code that rotates a volume 90 degrees clockwise about an axis looking from the positive end of the axis to the negative end of the axis.
(08 Jan 2007) Initial implementation of new Study Metadata File.
(08 Jan 2007) When loading a spec file turn off node highlighting (blue) cross.
(02 Jan 2007) Redesign of Identify Window. The window now has tabs that show the identification text or a page that shows the identification filtering selections. The filtering selections were previously on the window's toolbar.
(26 Dec 2006) Added volume yoking which is selected witht the Yoke button on a Viewing Window Toolbar. When on, the selected slices in the main window and the yoked viewing windows will be the same anytime a selected slices is changed by using the slice controls in the Toolbars or by identifying a voxel with the mouse.
(22 Dec 2006) When reading a Comma Separated Value File (such as one that contains foci), check for unicode's various dash codes (em-dash, en-dash, etc. 0x2010 to 0x2015) and underscores. If any are found convert them to minus signs. In addition, print a warning message for any text to floating point number conversions that fail.
(15 Dec 2006) Fixed bug in surface areal smoothing that set a node's XYZ coordinate to (0, 0, 0) if the node and its neighbors all have the exact same XYZ coordinate. The smoothing algorithm uses the area of triangles formed by a node and its neighbors and since the nodes all have the same XYZ coordinate, the area of these triangles was zero. The area of the triangles is used as a weight which results in the weighted average of the neighbor's coordinates becoming (0, 0, 0). Since we use a smoothing strength of 1.0, a smoothed node's new coordinates are entirely that of the neighbor's coordinates' weighted average. The smoothing algorithm now performs no smoothing of a node if the node and its neighbors all have the same XYZ coordinate. In particular, this problem was noticed with deforming a hull surface from one individual to another. It may also be the cause of occaisional problems noticed in multi-resolution morphing.
(13 Dec 2006) Add one-sample T-Test, Paired T-Test, and Interhemispheric Clusters to Statistical Algorithm Dialog.
(12 Dec 2006) On statistical algorithm dialog, enabled running of two-sample T-Test and Wilcoxon into Two-Sample T-Test operations. Split surface files and cluster search parameters into separate pages.
(12 Dec 2006) Add ability to run the metric/shape statistical permutation algorithms (one-sample t-test, two-sample t-test, paired t-test, etc.) using caret_command.
(11 Dec 2006) Add distance and (x,y,z) components to output metric file of the metric/surface shape t-map coordinate group difference.
(11 Dec 2006) Add opacity to border, cell, and foci display.
(11 Dec 2006) Add a polygon reduction option to caret_command's -volume-segment operation.
(08 Dec 2006) Enable the cluster search used in the shape/metric file statisical permuation algorithms to run as multiple threads in order to reduce execution time.
(08 Dec 2006) Modified SureFit segmentation algorithm so that it may produce volume types other than AFNI (such as NIFTI).
(06 Dec 2006) Allow a choice of symbols (OpenGL-points, squares, boxes, rings, spheres, diamonds) for border drawing.
(06 Dec 2006) Add "square" symbol for drawing foci. This is similar to the existing point symbol, except that the square scales with the size of the surface. This is unlike the Point symbol (which is draw using OpenGL's GL_POINT) which remains fixed in size even though the size of the surfaces changes.
(06 Dec 2006) Add median and abs-median to Surface Region of Interest Statistical Report.
(06 Dec 2006) Fixed crash that occurred if Caret was unable to open a file for writing.
(05 Dec 2006) Fixed problem in segmentation automatic error correction that prevented reporting of problems to the user due to an improperlay handled exception.
(04 Dec 2006) Fixed failure to display crossovers on initial flat surface at the end of flattening.
(01 Dec 2006) Add command line option "-notext" that disables OpenGL text rendering. Some Linux systems have a problem with the FreeType library that will cause Caret to crash.
(01 Dec 2006) Change XML file identification to look for the first ascii character that is not a space, tab, newline, or linefeed. If this first ascii character is a '<' it will assume the file is an XML file.
(28 Nov 2006) Modify GuiBrainModelOpenGL to delete the memory for BrainModelOpenGL when all windows are closed.
(27 Nov 2006) Added "Integrated Folding Index" to the Surface Region of Interest Dialog. Integrated Folding Index is for each surface shape column and equal to SUM(Ai * Fi) / SUM(Ai) where Ai is the area of a triangle and Fi is the average of the surface shape value's for the triangle's three nodes.
(22 Nov 2006) Added a new method named "crossover search" that searches for topological defects in a segmentation volume. This method operates by generating a spherical surface from the segmentation volume, smoothes the spherical surface, and then checks for crossovers in the spherical surface. Any crossovers are mapped into the segmentation volume's space to an RGB volume and to the RGB paint file on the surface.
(20 Nov 2006) Added -surface-to-volume option to caret_command for creating a volume from a metric/paint/shape surface file.
(20 Nov 2006) Speed up mouse processing for contour alignment translation on Linux and Windows.
(20 Nov 2006) Fix contour set scaling when the scaling has already been set.
(17 Nov 2006) Bug fix to make checkable the Enable Rotation on Volume->Transform menu item.
(17 Nov 2006) Changes to OpenGL code for offscreen rendering.
(16 Nov 2006) Added to the caret_command program: -caret-data-file-compare which compares the data contents of two Caret data files of the same type.
(15 Nov 2006) Enable volume yoking so that a volume in the Main Window may be yoked to a volume in one or more Viewing Windows. Yoking is selected by using the Yoke button in the Viewing Window(s) Toolbar.
(15 Nov 2006) Add button to Toolbar in Viewing Windows, label "UO" (Underlay Only), that is shown when the window displays a volume. If this button is toggled on, only the underlay volume is shown. This option has been added to assist in segmentation volume voxel editing where the Main Window contains an anatomical volume overlayed with the segmentation volume.
(15 Nov 2006) Had some problems with exceptions messages (such as an error reading a file) displaying incorrectly. Replacing C-character strings with QStrings seems to have fixed the problem.
(15 Nov 2006) Fixed some paint file reading error messages.
(14 Nov 2006) Fixed reading of NIFTI volume file when the orientation is not X={L,R}, Y={P, A}, Z={I, S}, such as AIL, so that the voxel sizes and spacing are correctly set.
(14 Nov 2006) When creating an MPEG1 or MPEG2 movie, check to see if the movie file name is writable. If not, pop up an error message. Unfortunately on MS Windows, if the file is writable but the directory is not writable, QT still reports the file as writable. The MPEG encoder will then crash Caret when it tries to open the movie file.
(13 Nov 2006) Looked into a problem with the colors being incorrect in the temporary images used to create a movie file with the program mpeg_create on MS Windows. The problem is that the bytes are being written in the wrong endian when writing the temporary PPM image file. However, the program mpeg_create expects them to be in this incorrect order, so, fixing the writing of the PPM images cannot be done as mpeg_create would no longer work correctly.
(10 Nov 2006) When saving a foci file, allow the user to choose saving of the original stereotaxic coordinates or the coordinates of the foci projected to left and/or right surfaces.
(10 Nov 2006) When a node is identified on a surface in a window, also show the coordinates of that node for surfaces displayed in other windows.
(09 Nov 2006) Fix error message for PALS foci projection when the foci's coordinate is invalid. Remove debug print message when saving a foci file.
(07 Nov 2006) Change version to 5.502.
(07 Nov 2006) Made a changes to Flatten Full Hemisphere so that there are not two compressed medial wall surfaces at the step in which the medial wall and cuts are edited.
(07 Nov 2006) When saving a topology file, default the topology file selected in the Save Data File Dialog to the topology file used by the main window surface.
(06 Nov 2006) When reconstructing contours into a surface, create a section file containing the sections corresponding to the nodes.
(06 Nov 2006) Popup a message when cleanup contours is run.
(06 Nov 2006) Fix View Current Files dialog so that border files are not always listed, even when no borders are loaded.
(06 Nov 2006) When a node was identified Caret was not updating the toolbar in windows viewing volumes.
(06 Nov 2006) When saving a foci file, allow the user to choose both left and right surfaces for the unprojection of foci projections into a foci file. Also, Caret was erroneously setting the file modification status of the foci projection file when saving a foci file.
(02 Nov 2006) When translating a surface using one of the Surface Menu->Transform menu items, do not transform cells or foci since they should be loaded as projection files.
(02 Nov 2006) Fix setting of contour Z-coordinate when drawing and reading contours.
(02 Nov 2006) Add identification symbols to contours. If a contour point highlighted and a surface is loaded, hightlight the corresponding node in the surface. If a node in the surface is identified, hightlight the corresponding contour point.
(02 Nov 2006) Replace left/right hemisphere checkboxes with a structure selection control on contour reconstruction dialog.
(02 Nov 2006) Change colors of contours to a darker green.
(01 Nov 2006) Add a cross at the origin of contour drawing.
(01 Nov 2006) Inhibit the drawing of cells in their original color and position when being aligned.
(01 Nov 2006) Slow mouse speed used during contour alignment.
(01 Nov 2006) Using a depth test for image drawing messed up surface rendering (See 31 Oct 2006). Instead, set the Z-value for the image near the far clipping plane.
(31 Oct 2006) Fixed bug that caused contours to disappear that were in the same section as that of a new contour being drawn while the new contour was being drawn.
(31 Oct 2006) Fixed bug that caused some contour cells to disappear when new contours in a different section were being drawn.
(31 Oct 2006) When drawing contours and only single section is being displayed, set the selected to the section of the new contour when drawing of the new contour is completed.
(31 Oct 2006) If the contour number in the draw contour dialog is changed, set the mouse mode to contour drawing.
(31 Oct 2006) Add legends describing necessary mouse clicks to Contour Set Scale Dialog. Fix setting of contour scaling.
(31 Oct 2006) Add Hide All Contours to Contour Selection Dialog.
(31 Oct 2006) Change image Z-value so that contours with negative Z-values show up in front of the image.
(30 Oct 2006) If mapping a NIFTI functional volume, add the intention and TR to the metric column comment.
(30 Oct 2006) Fix bug that caused Caret to crash if there were contours loaded and an MDPlot file was imported without appending selected.
(27 Oct 2006) Add a Help button to the Display Control Dialog that shows the dialog's help page.
(27 Oct 2006) Add the title of the Main Window's current spec file to the title of the Display Control Dialog.
(27 Oct 2006) Fix determination of caret installation directory for command line programs on Mac OSX.
(26 Oct 2006) Fixed reading of CSV foci file Study Info Comments.
(24 Oct 2006) Decrease the minimum scaling for contours so that the user may zoom out further.
(24 Oct 2006) Made fixes for reading MDPlot contour files.
(24 Oct 2006) Rewrote and moved identification code into BrainModelIdentification which is located in the BrainSet. This eliminates code duplicated in WebCaret and results in WebCaret showing the exact same text as Caret when an item is identified.
(20 Oct 2006) Add image comparison (-image-compare) to caret_command.
(19 Oct 2006) Add a flag to the BrainSet that is only set by WebCaret. If set and a scene file is read, paths associated with any file listed in the scene file will be removed. This is because SuMS stores all files associated with a spec file in a single directory.
(19 Oct 2006) Modifiy caret_command so that if it is run with "-help", a list of all of the commands is displayed. Running caret_command with "-help-full" will show full information on each command.
(19 Oct 2006) Modify caret_command's "-show-scene", "-show-surface", and "-show-volume" so that the volume file is optional, and, if not specified, the image of the scene/surface/volume is not saved in a file but is displayed in a window on the user's display.
(19 Oct 2006) Add "-image-view" to caret_command which displays an image file in a window on the user's display. Due to a limitation on Macs (the program is built as a simple executable and not a Mac Application), scrollbars are available only on Linux and Windows.
(19 Oct 2006) Add "-show-volume" to caret_command which generates an image of a volume.
(18 Oct 2006) When saving a scene, save the width and height of the OpenGL widget so that it may be used later when caret_command cxommands a scene for diplay. This ensures that the window size exactly matches the width and height of the saved window.
(13 Oct 2006) Add "-show-scene" to caret_command with renders the main window image of a scene to an image file.
(13 Oct 2006) When constructing a BrainSet from a topo/coord file pair, set the BrainSet's structure to that of the coord file.
(13 Oct 2006) Fix Spec File's remove paths from filenames.
(13 Oct 2006) Add "-show-surface" to caret_command which generates an image of surface in one or all of the standard views.
(12 Oct 2006) Make color names in the color key dialog appear as hyperlinks if vocabulary information is available.
(11 Oct 2006) Simplify cropping on the image editor window.
(11 Oct 2006) Fix default file naming for border and border projection files.
(11 Oct 2006) Use QT's QFile::errorString() when Caret is unable to read or write a file.
(04 Oct 2006) Fix removal of watch cursor when loading a border file through the open data file dialog.
(03 Oct 2006) Add an optional "point radius" to border and border projection links that will be used, in some cases, a variability measurement. Add two new Border Drawing modes that show the border link variability with or without connected line segments.
(03 Oct 2006) When generating average borders, also add a variability measurement to the links of the average border.
(03 Oct 2006) Add -surface-border-variability to caret_command that resamples a border file so that the borders have the same number of links as borders with corresponding names in another border file and set the variability.
(03 Oct 2006) Add -surface-border-nibbler to caret_command that remove links from a named border in a border file. The user may use a surface node or extrema to set a plane used for removing links.
(03 Oct 2006) Add -surface-border-extrema that lists the extrema (bounds) for a surface and a border in a border file and also shows the difference.
(27 Sep 2006) Fixed a bug with editing the comment in a multi-brick volume file on disk using the data file comment editor from the Open Data File Dialog. The bug resulted in the volume containing only one brick instead of all of the bricks in a multi-brick volume file. Now, none of the bricks are lost.
(27 Sep 2006) Fixed a bug that caused Caret to crash if a probabilistic atlas volume with only one channel was loaded.
(26 Sep 2006) Modify the node attribute selection combo box to prevent problems with it if there is more than one spec file loaded.
(25 Sep 2006) Add a new toggle button, labeled "S", to the toolbar that is displayed when viewing a volume. When the button is toggled on and the volume is being viewed in an orthogonal axis, the slice numeric controls instead show stereotaxic coordinates.
(25 Sep 2006) Use common widget for entering and editing studies for foci and vocabulary.
(25 Sep 2006) When loading a file via the Toolbar's "Spec" button, only ask Append/Replace if there is data of the corresponding type loaded.
(25 Sep 2006) Change Caret version to 5.501.

Release Caret 5.5 (22 September 2006)

(22 Sep 2006) Add Layers->Borders->Create Borders From Paint Regions which creates borders around all paint regions in a selected column. It will probably work best on a surface with a closed topology.
(20 Sep 2006) Fix setting of column names for old, old, version 0 paint files.
(20 Sep 2006) Change Layers->Foci->Delete Non-Displayed Foci to "Delete Foci Not Displayed on Main Window Surface". When choosing foci for deletion, also use status of show foci on correct hemisphere only option.
(20 Sep 2006) Fix problem with reading files containing long lines. This problem was traced to a bug in Trolltech's QT Software (http://www.trolltech.com/developer/task-tracker/index_html?method=entry&id=104776) which would only read the first 4095 characters in a line. So, any files with lines longer than 4095 were not read correctly.
(19 Sep 2006) When creating a new spec file on the spec file dialog, close current spec file and reopen the new spec file into a new spec file dialog.
(19 Sep 2006) Require a volume's existing voxel sizes to be positive and the resampling voxel sizes to be positive.
(19 Sep 2006) When saving a volume file using the Save Data File Dialog, default the volume to the volume of the selected type that is selected on the Display Control Dialog's Volume - Overlay/Underlay page.
(19 Sep 2006) Enable double-clicking of a cell in the file viewing table for editing the cell's contents in a text editor.
(19 Sep 2006) Multi-Fiducial Metric Mapping changes: (1) Default column names are now AFM for average fiducial mapping and MFM for multi-fiducial mapping. When available, include hemisphere in column name. (2) Default comments are now "Average Fiducial Mapping (AFM)" and "Multi-Fiducial Mapping (MFM)". (3) The cells in the metric naming table may be double-clicked to display and more easily edit the cell's text.
(15 Sep 2006) Fixed writing of cell/foci files in Comma Separated Value (CSV) file format.
(15 Sep 2006) Fixed bug that produced some print statements when saving a border file.
(14 Sep 2006) Change key command used to capture an image of caret dialogs to CTRL + SHIFT + F1.
(14 Sep 2006) Fixed crash that occurred if capturing an image of part of the main window but without any of the main window selected.
(12 Sep 2006) Improve text editor with better search options. Pressing the Find toolbar button brings up a dialog for searching and replacing include case sensitive and backwards searches.
(12 Sep 2006) Add generation of a border grid for analysis with a third party program.
(12 Sep 2006) Add foci highlighting. A focus is highlighted by clicking on the foci's color in the Foci Color Key Dialog.
(12 Sep 2006) Add vocabulary abbreviations to name selection dialog.
(12 Sep 2006) Fix Surface->Transform->Apply Current View when both translation and rotation were applied.
(12 Sep 2006) Got shell command window to work on Windows.
(11 Sep 2006) Modify Interpolate Surfaces so that it applies the current view to the surfaces used for interpolation.
(11 Sep 2006) Fix Edit Paint Names Dialog.
(11 Sep 2006) Fix deletion of probabilistic atlas file on view current files dialog.
(11 Sep 2006) Save override border colors with area colors to scene.
(11 Sep 2006) Correct Metric/Shape statistics dialogs that mistakenly read "Type II Error" but should have been "Type I Error".
(08 Sep 2006) Change version to 5.5.
(08 Sep 2006) Add Vocabulary Editor to Attributes Menu. If the user clicks on a name in a color key and there is a corresponding entry in the vocabulary file, information from the vocabulary file will be displayed in the Identify Window.
(07 Sep 2006) Made some changes to reading of cells/cell projections from comma separated value files.
(06 Sep 2006) Have Identify Window's CID button clear both border highlighting in addition to node highlighting.
(05 Sep 2006) Change border and paint color keys so that if the user clicks on the color swatch, the nodes are highlighted or the border point/line size is doubled. Clicking on the color swatch of a highlighted item turns of highlighting. Add item to Layers->Borders menu and popup menu to clear border highlighting.
(05 Sep 2006) Add menu item to Attributes->Vectors Menu that copies the main window surface's normal vectors to the surface vector file.
(01 Sep 2006) Fixed scene problem with node attribute files (metric, paint, etc.) when the number of surfaces loaded exceeded the number of columns in the node attribute file.
(01 Sep 2006) When generating an areal estimation file, add the border file and uncertainty value to the comment.
(01 Sep 2006) Increase far and near values for orthographic projection so that the surface does not get clipped as quickly and user can zoom in further.
(01 Sep 2006) Add coordinate files for PALS SPM95 and SPM96 to mapping files for use by PALS foci projection.
(01 Sep 2006) Add SPM96 and MACAQUE_F6 to stereotaxic spaces.
(31 Aug 2006) Add color key displays to the popup menu.
(31 Aug 2006) Add color key windows to scenes.
(31 Aug 2006) Add an areal estimation page to the Display Control Dialog so that column names may be changed.
(31 Aug 2006) Add Color Keys for Areal Estimation, Probabilistic Atlas, Volume Paint, and Volume Probabilistic Atlas.
(30 Aug 2006) Add option to Display Control Dialog's Border Page, that overrides border colors with area colors.
(30 Aug 2006) Upgrade QT on Mac to 4.1.4.
(30 Aug 2006) Add some additional file filters to the text editor's open/save dialogs.
(29 Aug 2006) Fixed file filters so that existing files are displayed on Capture Image of Main Window Dialog's file selection dialog.
(29 Aug 2006) Increase width of scene selection box on Display Control Dialog.
(29 Aug 2006) Move "CID" button (clears ID symbols from surface) to the left side of the Identify Window so that is easier to access.
(29 Aug 2006) Modify interpolate surfaces dialog so that the number of surface selections is equal to the number of surfaces that are loaded.
(29 Aug 2006) Fix problem with the surface radically changing size at the end of the interpolate surfaces action.
(29 Aug 2006) Add color key dialog for borders, cells, foci, and paint. The color key dialog shows the names of all displayed items and a swatch of the assigned color.
(28 Aug 2006) Add a new metric selection option on the Display Control Dialog. If the "L-to-L, R-to-R Matching..." checkbox is selected and the user selects a metric column, look in the selected column's name for "left" (or "right") and and apply it to all left (or right surfaces). Then, find the corresponding column for the other hemisphere and apply it to the remaining surfaces.
(28 Aug 2006) Fixed saving of Paint Medial Wall Override to a scene.
(11 Aug 2006) Add spherical deformation to the caret_command command line program.
(11 Aug 2006) Add optional surface shape file that will contain uncertainty to caret_command -surface-average.
(11 Aug 2006) Add item to Layers->Foci menu that deletes all colors that do not match the start of any foci name.
(10 Aug 2006) Add a Surface Distance metric/shape test to the Metric/Shape Statistical operations menu.
(09 Aug 2006) Add surface smoothing to caret_command.
(09 Aug 2006) Add item to Layers->Foci menu that deletes all non-displayed foci.
(07 Aug 2006) In metric/shape statistical operations, use the topology file specified by the user. Note: some coordinate files contain the name of a topology file in the header that is automatically loaded and assigned to the coordinate file when the coordinate file is loaded.
(04 Aug 2006) Add button on Display Control's Scene Page "Create Spec From Selected Scenes" which prompts the user for a scene file name and a spec file name. This creates a new scene file containing only the selected scenes and a spec file containing the files from the selected scenes.
(04 Aug 2006) Change Check All Scenes so that it unloads all file prior to estabilishing a scene.
(04 Aug 2006) Fix ID window text problem that resulted in new text being blue and underlined if a hyperlink had been clicked.
(03 Aug 2006) Add a new surface shape selection option on the Display Control Dialog. If the "L-to-L, R-to-R Matching..." checkbox is selected and the user selects a surface shape column, look in the selected column's name for "left" (or "right") and and apply it to all left (or right surfaces). Then, find the corresponding column for the other hemisphere and apply it to the remaining surfaces.
(03 Aug 2006) Change message on Display Control's Scene page when unloading all files but spec and scene.
(03 Aug 2006) When a focus is identified, display its position on all fiducial surfaces with valid stereotaxic spaces.
(03 Aug 2006) Fix crash if trying to access a color but no colors are loaded during probabilistic atlas coloring.
(03 Aug 2006) Fix normal/threshold probabilistic atlas selection on Display Control.
(03 Aug 2006) Remove min/max section numbers from Main Window Status Bar.
(03 Aug 2006) Change cell and foci left/right display to a single check box Show Cells/Foci on Correct Surface only.
(01 Aug 2006) Add section control to scenes.
(01 Aug 2006) Do not require a class when entering foci on the map stereotaxic foci dialog.
(01 Aug 2006) Transformation Matrix Dialog, attempt to get new matrices created with oblique volume views to work.
(01 Aug 2006) When a voxel is identified in volume montage display, center the selected volume slice in the montage.
(31 July 2006) Fix voxel identification for volume montage viewing mode.
(31 July 2006) Change volume montage slice orders to that the slices increase going right to left and then down to the next row of slices.
(31 July 2006) Allow main window transformation axes to be turned on/off by clicking on the axes in any of the viewing windows.
(31 July 2006) Make volume crosshairs consistent so X is red, Y is green, and Z is blue.
(28 July 2006) Add projection of Foci to PALS atlas. Foci are mapped to the surface that is in the same stereotaxic space as the focus.
(27 July 2006) Fix shortcut keys for Identify and Transformation Matrix Editor menu items on Windows menu.
(27 July 2006) On transformation matrix editor and applying a transform, have cancel button cease the process.
(24 July 2006) Add Levene's Test for Equality of Variance to Metric/Shape Statistical processing.
(24 July 2006) Use Dcdflib for statistical P-Value computations (http://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware.aspx?Software_Id=21).
(21 July 2006) Reorganize/rewrite statistical functions and place them in their own library.
(18 July 2006) Make text boxes for scene names wider on Display Control Dialog.
(18 July 2006) Add item to Caret Help Menu to search the Caret website.
(18 July 2006) Fix default directory selection on Copy Spec File Dialog and add a previous directory selection.
(18 July 2006) Add comment button to Spec File Dialog.
(18 July 2006) Upgraded the Linux version of QT to 4.1.4. This appears to correct a bug that caused Caret to crash on startup when the style being used was Plastique. Only some Linux systems default to the Plastique style and I do not know how this is chosen.
(18 July 2006) Added preliminary support for storing cells and foci as comma separated value (CSV) files.
(14 July 2006) Fixed computation of P-Values when the T-Value is less than zero.
(13 July 2006) When using the CTRL-Escape Key (Apple-Escape Key on Macs) which captures an image of any caret dialog or window, allow the user to choose to copy the image to the clipboard, print the image, or save the image to a file.
(13 July 2006) Add one more bucket to histogram so that all values are shown (largest value was at left side of last bucket).
(13 July 2006) Make range of X-min/max unlimited on graph dialog.
(13 July 2006) Add False Discovery Rate to T-Map generation dialog (this may get changed soon).
(12 July 2006) Fix crash when displaying Volume Region of Interest Dialog.
(12 July 2006) Fix surface shape clustering and smoothing.
(11 July 2006) Add help buttons to metric/shape statistics dialogs that link to appropriate help page.
(10 July 2006) Change style of Caret data file XML headers to remove limitations on header tag name characters.
(10 July 2006) Add some additional stereotaxic spaces: T88, SPM, SPM95, SPM5.
(07 July 2006) Add comment section to Create Spec File Dialog and SureFit Segmentation Dialog. Add View/Edit comment to Open Spec File Dialog.
(07 July 2006) Add ticks in second plane for surfaces axes and add an offset for the surface axes controlled through the Display Control's Surface Miscellaneous page.
(07 July 2006) Mac OSX Only - Modify QT source for Q3FileDialog to set the style of the Filter Combo Box to Plastique since Mac style is way to long and stretches off the screen.
(07 July 2006) Fix error that made histogram dialogs modal.
(07 July 2006) Allow Set Topology Dialog to remain displayed at all times instead of closing upon topology selection.
(05 July 2006) Change the decimation algorithm from vtkDecimateCaret to vtkDecimatePro. vtkDecimate was dropped from VTK version 5 so I converted it to work with VTK5 but it was difficult to control the polygon count and it is a patented algorithm. vtkDecimatePro produces very similar surfaces with a slightly smaller polygon count the VTK4's vtkDecimate. vtkDecimatePro is easier to use with non-human surfaces and there are no patent issues with vtkDecimatePro.
(05 July 2006) Fixed bug in the math utilities function signedDistanceToPlane when converting floats to doubles in order to call a VTK math function. This bug caused a problem with sulcal depth generation.
(05 July 2006) Add option (defaulted on) to the Spherical Deformation Dialog to enable one iteration of smoothing of deformed coordinate files (except flat coordinate files). Previously, one iteration of smoothing was always performed. Option also added to Apply Deformation Map Dialog.
(03 July 2006) Surface Registration Fixes: First, when creating the deformation map file, indicate the type of surface (flat or spherical) to BrainModelSurfacePointProjector so that it can properly projection target nodes onto the deformed source surface. Second, the deformation map file always has the closest of the three source nodes listed first. When the first node was not the closest, the nodes and barycentric areas were being swapped but the barycentric areas were not properly swapped. These problems were first noticed when the source surface had far fewer nodes than the target surface.
(30 June 2006) Add Caret Tips Window which is selectable from the Help Menu and is automatically displayed (but can be disabled) after loading the first spec file in a caret session.
(30 June 2006) Update graphics window's popup menu.
(29 June 2006) Update the Mac Application for File Open Event.

Release Caret 5.402 Update (29 June 2006)

(29 June 2006) Fix Display Control's Surface Shape Min/Max mapping spin boxes so that they allow negative values
(28 June 2006) Now version 5.402.
(28 June 2006) Fixed bug that caused the current directory to be set to the caret installation directory during SureFit Segmentation. This typically occurred if caret was started in a directory other than the directory containing the volume for segmentation such as on Window when double-clicking a shortcut to Caret on the Desktop.
(28 June 2006) Allow several surfaces, in addition to the average fiducial, to be shown over the volume slices.
(27 June 2006) Add variance smoothing to metric and shape file statistical operations.
(27 June 2006) Copied and modified VTK's vtkMPEG2Writer class so that it writes MPEG1 video files. This allows Mac users to create MPEG movies that are playable by the standard version of QuickTime media player. It also eliminates the need to use the command line program mpeg_create to create movies although it is still supported. This will also help windows users since mpeg_create often crashed or hung when creating movies.
(26 June 2006) Added an active hull surface that may be displayed over volume slices.
(26 June 2006) Updated caret_command to combine surface shape files.
(26 June 2006) Added Surface->Measurements->Generate Distance: Surface A to Surface B which creates a surface shape column that contains the three-dimensional distances between two surface's coordinates.
(23 June 2006) Added MPEG2 movie writing using a VTK class. At this time, only the latest Windows Media Player run on MS Windows and mpeg2play on Linux can play MPEG2. According to Apple, an upgrade to Quicktime (that cost $) will allow Quicktime to play MPEG2 movies.
(22 June 2006) Change File Menu's "Record as MPEG" to "Record Main Window Images as Movie".
(22 June 2006) If the user attempts to map an ".hdr" volume to a surface, warn the user that the volume must contain an SPM originator to be mapped correctly.
(22 June 2006) Enable/Disable menu items using QT4.
(22 June 2006) Replace vtkDecimate with vtkDecimateCaret since vtkDecimate was dropped from VTK5. There might be polygon reduction issues with rodent brains. Upgrade to VTK5.
(21 June 2006) Replace QtFloatSpinBox with QDoubleSpinBox.
(21 June 2006) Compiled with QT3 support off to eliminate calls to class methods that are not QT4 compatible. QT4 conversion will be complete once additional widgets can be added to QFileDialog.
(19 June 2006) When text added to Identify Dialog automatically scroll to the bottom of the text.
(19 June 2006) Fixed loss of cell class information when projecting or unprojecting.
(16 June 2006) Add capture of 6 standard view image to Capture Image of Main Window Dialog.
(16 June 2006) Upgraded Recording Dialog to QT4.
(16 June 2006) Add a page to the SureFit Segmentation Dialog that shows the current directory and prevents the user from continuing if the current directory is the caret installation directory. The current directory may be the installation directory if Caret was started by a shortcut on the Windows Desktop or from the Mac's Dock.
(16 June 2006) Add a menu item for reverse the order of points in a contour.
(15 June 2006) Added drawing modes for contours so that contours may be drawn as lines, points, or points and lines. If drawing the first contour point in red, make the first contour point size double that of the normal contour points.
(15 June 2006) Fixed crash that occurred when adding a new color using the Edit Colors dialog.
(15 June 2006) Upgraded SuMS Database Dialog to QT4.
(15 June 2006) On Surface to Volume Dialog, change "Thickness Step" to "Intersection Step".
(14 June 2006) Now version 5.401.
(13 June 2006) Added identification of contours and contour cells in view mode. Enhance legends for contour append mode.
(13 June 2006) Upgraded code for Map Volumes To Surfaces to QT4.
(12 June 2006) Upgrade to QT 4.1.3. This seems to have corrected problems with windows popping up under the current window on Macs and fixed directory selection problems when using Set Current Directory from the File Menu.
(09 June 2006) Fix problem with copy/zip spec file when the volume consisted of a header file and a volume file and the volume was in a different directory than the source spec file.

Release version 5.4 (09 June 2006)

(09 June 2006) Destroy the SureFit Segmtation Dialog when it is closed so that segmentation can be restarted without having to exit and restart caret.
(08 June 2006) Version 5.4
(08 June 2006) Handle http URL's in Caret web help by displaying the page in a web browser.
(07 June 2006) Fixed writing of gzipped volume files on Windows by updating the zlib library and using buffered writing instead of unbuffered writing.
(05 June 2006) On Volume Math Dialog, change "Volume C" to "Volume Output".
(05 June 2006) When loading a scene, do not load any scene file from the spec file saved within the scene.
(05 June 2006) Move shape file statistical processing from Surface Shape Menu to new Metric and Shape Statistical Processing Menu.
(05 June 2006) Save data file timeout from SuMS Dialog in the preferences file.
(05 June 2006) When adding a new color, place it in its name sorted position.
(02 June 2006) Correct problem with uploading volume data files to SuMS.
(02 June 2006) Add one-sample and two-sample T-Tests for Metric and Surface Shape.
(01 June 2006) Correct problems with interpolate surfaces not updating the model in the main window.
(31 May 2006) When displaying a scene, do not let viewing windows to be shown off the screen.
(30 May 2006) When mapping to the Average Fiducial Surface, set the column threshold to the threshold entered for the respective functional volume.
(30 May 2006) Correct uploading of volume data files to SuMS.
(25 May 2006) Add NIFTI gzipped file to volume files supported by script builder.
(25 May 2006) Disable image file save dialog if there are no image files loaded.
(23 May 2006) Fix writing of WU NIL volumes on little endian architectures (Intel x86, typically windows and linux).
(22 May 2006) Fixed problem with loading a Hull Coord File using the Open Data File Dialog.
(22 May 2006) Added scroll bars to Volume Math Dialog since dialog was getting too tall.
(18 May 2006) Added missing '*' to .ifh volume file filters.
(18 May 2006) Add update deformation path, create spec file, and add file to spec file to the script builder.
(18 May 2006) Remove message about undo stack size printed when editing segmentation voxels.
(17 May 2006) Now version 5.332.
(17 May 2006) Fix display of web page when a hyperlink is clicked in the file comment editor (QT4 upgrade problem).
(17 May 2006) Make sure a display list is valid prior to deleting it.
(17 May 2006) Remove multiple sets of scrollbars from Display Control Dialog.
(16 May 2006) Add Clean Up Contours to the Layers->Contours menu. Clean Up Contours will remove consecutive, duplicate points from contours and it will remove contours with less than 3 points. These types of contours cause problems during reconstruction.
(16 May 2006) Replace line edits with spin boxes on Surface to Volume Dialog..
(16 May 2006) Restore volume animation that was broken during upgrade to QT4.
(16 May 2006) When adding a volume file entry to a spec file, only write the data file name if it is different than the header file name (ie: NIFTI volume is stored within a single file).
(16 May 2006) Scene modifications: track volume oblique slice sampling size and the matrices associated with transformation data files.
(15 May 2006) NIFTI volume reading and writing including zipped files, paint volumes, and support for the AFNI extension.
(12 May 2006) Add "plus_" and "minus_" to name in the paint created by the Find Significant Clusters operation.
(12 May 2006) Fixed bug that prevented mapping to average fiducial surface using the map volume to surface dialog.
(09 May 2006) Fix spec file update when the volume header file name is the same but the data file name changes.
(03 May 2006) When page selection changed on Display Control Dialog, scroll the page to the left and top.
(02 May 2006) Corrected problems with left hemisphere foci not appearing.
(27 April 2006) Improved support for reading and writing NIFTI volume files.
(21 April 2006) Eliminated all QT 3 version support code from the Display Control Dialog. This appears to have corrected two problems. The first correction eliminates lots of little windows (border names, colors, foci, etc checkboxes) from appearing prior to the Display Control Dialog. The second correction appears to eliminate the very slow time (minutes) that elapsed while displaying the dialog on computers with limited amounts of memory.
(17 April 2006) Add option to caret_command that sets the source and target paths.
(13 April 2006) Now version 5.331.
(12 April 2006) Fixed bug found in shape file T-Map calculation that occurred if the first shape file had fewer columns that the second shape file.
(04 April 2006) Replace Volume Animate start/resume/pause/stop with a single Animate button that goes through all slices. This change has been made because the volume animate thread does not work in QT4.
(03 April 2006) Fix triangle area calculation that was replaced vtk's triangle area a few days ago.
(03 April 2006) Fixed problem with bizarre characters in surface region of interest report.
(31 March 2006) Fix editing of file column comments.
(31 March 2006) Move Image Editor and Text File Editor menu items from the File Menu to the Window Menu.
(31 March 2006) Fix initial directory on Zip Spec File dialog's choose zip file button.
(31 March 2006) Replace use of function tmpnam() and replace with QDir::tempPath(). tmpname() is a possible security hole.
(31 March 2006) Add printing, font selection, and search/replace to text editor.
(31 March 2006) Fix creation of wrong column on metric/shape inclusive range operations.
(29 March 2006) When merging contours, beep if a contour is not selected with a mouse click. In addition, when two contours are merged, resample the new contour so that the region between the contours will contain points.
(29 March 2006) Started adding an "index tree" to the help window.
(27 March 2006) Fixed problems with absolute paths that should not have been on files added to the spec file in the windows version of caret.
(27 March 2006) For file open/save/import/export dialogs, set the directory to the current directory.
(27 March 2006) Add application of a deformation map to a data file to caret_command.
(24 March 2006) Fix selection of contour cells when aligning a region of a contour.
(24 March 2006) Change contour region box from solid to outline so that contours/cells are visible.
(24 March 2006) Warn that contour region alignment will not function if contours are rotated.
(24 March 2006) Fix writing of WU ".ifh" header files.
(17 March 2006) Fix reading of version 1 cell projection files.
(17 March 2006) Fix bug that failed to create new metric/shape column in mathematical operations.
(17 March 2006) Work around QT4 bug that prevented reading of version 0 cell files.
(17 March 2006) Fix bug with missing items on image editor resize dialog.
(16 March 2006) Force all volumes written by surefit segmentation process to be written as floats.
(16 March 2006) Fixed Display Control images selection page on windows.
(16 March 2006) Work around QT4 bugs for SuMS file transfers.
(13 March 2006) Fixed bug that prevented writing a file when the all files preferred write type and the files read type were the same but not acceptable for an output format.
(13 March 2006) Fixed crash when combine paint volumes was selected on Volume Mathematical Operations Dialog.
(13 March 2006) Third volume optional on volume math with script builder.
(13 March 2006) Shrank font for node number on ID dialog.
(13 March 2006) Fixed bug on script builder that prevented creating the script without executing the command.
(13 March 2006) Fixed crash that caused Caret to crash when saving a coordinate file.
(10 March 2006) Fix bug that listed an invalid cerebral hull volume as a segmentation volume.
(10 March 2006) Fixed script builder.
(10 March 2006) Put updated mingwm10.dll in windows distribution.
(09 March 2006) Since caret cannot handle scenes with more than one spec file, do not allow a scene to be created if there is more than one spec file loaded.
(09 March 2006) Add checks for invalid surface type or topology type when importing a surface file.
(09 March 2006) Add generation of sulcal depth to caret_command.
(07 March 2006) Fix crash when loading a paint file for a scene. This is a QT4 bug.
(07 March 2006) Fix missing Metric Mathematical Operations.

Release Version 5.33 03 March 2006

(03 March 2006) Fixed display of caret help on Windows.
(03 March 2006) Changes to set directory dialog.
(03 March 2006) Fix crash when space button pressed on Create Spec File Dialog.
(02 March 2006) Move caret_morph command line program operations in caret_command.
(01 March 2006) Add projection and unprojection of cell and foci data.
(01 March 2006) Add projection and unprojection of borders to caret_command program.
(01 March 2006) Add new dialog for capturing an image of the main window to the file menu. The menu item is named Capture Image of Main Window. The dialog allows the user to capture an image of the entire main window or a region selected with the mouse. The captured image may be copied to caret's loaded images, copied to the clipboard so that it can be pasted into other programs, printed, and/or saved to a file.
(27 Feb 2006) Update Linux compiler to GCC 4.0.2 with static libraries to fix crash on some Linux systems with shared object libraries different that out build system. This fixes the failure to catch exceptions that were thrown.
(24 Feb 2006) Fix crash in spherical deformation if the original coordinate file contained a full path in its name.
(24 Feb 2006) Default align sphere checkbox checked on align surfaces dialog.
(22 Feb 2006) Add conversion between caret paint file and free surfer label files to caret_file_convert.
(21 Feb 2006) Add ability to generate inflated, ellipsoid, et al using caret_command.
(21 Feb 2006) Add generation of hull surface when determining sulcal depth.
(21 Feb 2006) Added some kludges to get around bugs in QT4.1 that prevented writing caret files in binary format. All file writing preference to be set to binary.
(20 Feb 2006) Figured out how to create simple executables for command line programs on Mac OSX instead of app bundles.
(14 Feb 2006) Replace "QtPlot" graphs with Qwt graphs.

(13 Feb 2006) The QT4.1 bugs appear to also cause problems with writing files in binary format. So, for now, the preferences always report that the user wants to write ASCII format files.
(13 Feb 2006) There are bugs in the QT4.1 software that cause it to report invalid file read position and end of file status. Code has been added to Caret5 to get around this bug until Trolltech (the writer of the QT software) corrects the problem. All of the added code is within "#define QT4_FILE_POS_BUG".
(13 Feb 2006) For all color files, add the color for "???", the unknown color, when the first color is added to the color file.
(10 Feb 2006) Modify caret_command so that it can add files to a spec file.
(09 Feb 2006) List the name of the spec file on the File Menu's Close Spec File menu item.
(07 Feb 2006) Convert SpecFile dialog and other dialogs to QT4 to fix problems on Windows.
(06 Feb 2006) Fixed problem with JPEG and QT 4.
(06 Feb 2006) Added a FreeBSD version of Caret5 to the download page. This version was built by Jason at MCW.
(06 Feb 2006) Limit sizes of dialog windows to less than the height of the desktop.
(06 Feb 2006) When a scene is selected, do not alter the main window and position other windows relative to the main window.
(06 Feb 2006) Add selection for surface and topology types on Import Data File dialog.
(01 Feb 2006) Add importing of Free Surfer binary format "curv" files.
(01 Feb 2006) Add importing of Free Surfer binary format "w" (weight, functional) files.
(01 Feb 2006) Add importing of Free Surfer binary format surface and surface patch files.
(31 Jan 2006) Replace FileOperationException and FileIOException with FileException.
(31 Jan 2006) Make some qmake .pro fixes for the elimination of Borland C++.
(30 Jan 2006) Split toolbar into two rows with model selection control in the bottom row.
(30 Jan 2006) Modify file reading to throw exception if reading a binary format Caret file due to a bug in QT4. Similar problem with version 0 topology file.
(30 Jan 2006) Modify the multi threaded algorithm class to avoid unlocking mutexes due to a bug in the QT4 windows software.
(27 Jan 2006) Change Identify Sulci process in SureFit Segmentation. When determing the sulci for paint geography, use the CerebralHull.erode.3 volume (the cerebral hull eroded three times) instead of Sulci.3.dilate.
(26 Jan 2006) In Segmentation voxel editor, the size of "undo's" was unlimited. Now, the total "undo" size is limited to 10 Meg with a minimum of one item. This will hopefully fix some crashes that have occurred during voxel editing.
(26 Jan 2006) Correct problem in error measurements at beginning of automatic error correction noticed on Windows.
(24 Jan 2006) Add item to surface menu that creates a segmentation volume from a surface.
(24 Jan 2006) Move script builder from Volume Menu to Window Menu. Command line program caret_volume has been renamed to caret_command since it now performs non-volume operations.
(23 Jan 2006) Prevent possible crash in TopologyHelper with a nodes that has zero neighbors. Crash is noticed on Windows Caret while creating inflated surfaces.
(13 Jan 2006) Add support for universal binaries (power pc and intel architectures) for Mac OSX.
(12 Jan 2006) Upgrade Caret5 to use user interface software QT 4.1 (www.trolltech.com). Caret5 runs but a QT bug prevents proper file reading.
(11 Jan 2006) Replace all uses of std::string with QString.
(06 Jan 2006) Add ability to load multiple spec files into Caret. All brain models are available for display. In addition, if multiple spec files have been loaded and there are at least two active fiducial surfaces, add a selection to show all fiducial surfaces simultaneously.
(04 Jan 2006) Correct 3D border drawing when metric and/or shape color palette bars are displayed.
(01 Jan 2006) Happy New Year !!!
(30 Dec 2005) Remove widget names from QT constructors in preparation for conversion to QT4.
(29 Dec 2005) Fixed bug in caret_volume and Caret's Volume Mathematical Operations that always caused a non-matching dimensions error.
(29 Dec 2005) Remove OSX_COMPILER_BUG stuff since compiler on Mac was fixed long ago to properly initialize std::string that are a static member of a class.
(29 Dec 2005) Consolidate stereotaxic space, species, category, and structure code.
(28 Dec 2005) Changes made to SpecFile code internals to support multiple structures.
(23 Dec 2005) Add optional distortion correction via a metric column for surface region of interest statistical report.
(20 Dec 2005) Fixed bug that caused a data file to be reported modified when it had not been modified but just copied.
(20 Dec 2005) For scenes, default window placement to leave main window at its location but place all other windows relative to the main window.
(19 Dec 2005) Modified Interpolate Surfaces so that surface scaling is interpolated. Previously, the scaling of the first surface in the sequence was used for all surfaces in the sequence.
(19 Dec 2005) Correct bug on Windows that caused problem with Automatic Rotation Dialogs fixed rotation spin box.
(19 Dec 2005) On Volume Attributes Dialog and Surface to Volume Dialog there is an option to get paramters from a volume file. This option now converts the parameters read from the volume file to an LPI orientation.
(15 Dec 2005) Fixed some problems that were found with NIFTI file format during various Caret operations.
(15 Dec 2005) When reading a VolumeFile and determining its file type by using the file's extension, convert the extension to lowercase since MS Windows or the SFTP client we use seems to sometimes make ".HEAD" files into ".head" files.
(13 Dec 2005) Implement preliminary NIFTI Data File format for Coordinates, Topology, Metric, Shape, Paint, and Probabilistic Atlas. For Node Data files, each column is stored in a separate piece of memory rather than one huge contiguous piece. The NIFTI files may also be read and written in XML format.
(2 Dec 2005) Install kludge to get around strange problem on windows. Creating movies of a flat surface resulted in smeared images. The problem was narrowed to the fact that lighting was off. So, when capturing movies on windows of a flat surface, turn lighing on prior to capturing an image of the flat surface and turn lighting off after capturing an image of the flat surface.
(1 Dec 2005) Add Find Interhemispheric Clusters to Attributes:Surface Shape menu.
(1 Dec 2005) Surface Shape Find Significant Clusters: allow metric or shape file for distortion correction file.
(1 Dec 2005) Fix install script on Mac OSX so that it does not try to set permissions on the no longer existing "luts" directory.
(30 Nov 2005) Show thresholds on Surface Shape Significant Cluster report.
(22 Nov 2005) Fixed problem with reconstruction of primate brains from volumes with unusual voxel sizes on Windows. Solution was a new version of VTK (see 17 Nov 2005).
(22 Nov 2005) Add a new Palette, "PSYCH-NO-NONE", that is similar to the PSYCH palette but does not have the NONE color.
(22 Nov 2005) Fix metric coloring so that nodes that are between pos-min and neg-min are not colored. Update labels on Display Control to add ">" to pos-min and "<=" to neg-min.
(22 Nov 2005) Surface Region of Interest Dialog: Add "And Not" selection which selects nodes that are currently selected but NOT selected in the new selection. Allow creation of new metric and surface shape column when assigning the respective values.
(22 Nov 2005) Surface Shape Find Significant Clusters: compute degrees of freedom and p-value for t-map and only use the biggest cluster from each of the shuffled t-maps.
(18 Nov 2005) Add non-uniformity correction to Edit Volume Attributes: Data page.
(18 Nov 2005) Add surface offset to volume script builder's Intersect Volume With Surface.
(17 Nov 2005) Surface reconstruction from volume polygon decimation is now optional but decimation is defaulted on. The decimation algorithm is failing to work properly on one PC with several primate species.
(14 Nov 2005) Fix palette color bar for functional volume viewing.
(11 Nov 2005) Fix deleting of all contours.
(11 Nov 2005) Prevent crash if reconstructon from contours fails.
(11 Nov 2005) Correct display of contours on oblique volume slices.
(11 Nov 2005) Correct filtering of contour cells on Spec File Dialog.
(10 Nov 2005) Fix editing of segmentation and paint volumes when "ALL" slices are viewed in the main window.
(9 Nov 2005) Add AC-PC alignment to Edit Volume Attributes dialog.
(8 Nov 2005) Add adjustable sampling for oblique volume slice viewing to Display Control's Volume Settings page.
(8 Nov 2005) Add contour and contour cell files to the list of available transform data files.
(7 Nov 2005) Change error message when orienting a surface so that a paint named set of nodes is oriented away from the user. This primarily occurs if the user is trying to flatten a partial hemisphere and the CUT.FACE nodes are not identified.
(1 Nov 2005) Fixed bug with deformation file naming that occurred if the output spec file listed in the deformation map contained a path.
(1 Nov 2005) Fixed bug with deformation of a coordinate file that occurred if the topology file could not be read.
(25 Oct 2005) In full hemisphere flattening, moved straggler tile removal to prior to pushing the sphere flat. This corrects a problem with a node along surface edge being dragged to the origin.
(24 Oct 2005) Use only selected shape columns for surface shape cluster analysis report.
(24 Oct 2005) Contour alignment and MDplot import fixes.
(12 Oct 2005) Multi-Fiducial Mapper - Fixed anomoly that if only mapping to the averaged coord file, the algorithm was still mapping to all of the individual cases.
(12 Oct 2005) On Spec File Dialog, change the Select All and Deselect All push buttons so that they only select or deselect files that are currently shown using the file display filter toolbar buttons.
(11 Oct 2005) Fix zooming of oblique volume slices.
(11 Oct 2005) When in view mode and a transformation axis is selected, avoid performing any ID Node or Voxel operations.
(10 Oct 2005) Add metric deformation (nearest node or average of nodes) to Apply Deformation Dialog.
(10 Oct 2005) Corrected numerics on metric palette color bar when user scale is selected with the positive or negative minimum not eqaul to zero.
(07 Oct 2005) Fixed problems with display of oblique volume slices and transformation cells on the oblique slices.
(06 Oct 2005) Add a Model Editor that allows the color of the VTK Models to be changed. This coloring now includes opacity.
(06 Oct 2005) Removed transformation matrix editor from the Surface and Volume menus and placed it on the Window Menu.
(06 Oct 2005) Add opacity to VTK models.
(06 Oct 2005) Fix writing of VTK models in ascii format.
(05 Oct 2005) Add Log base 2 to metric/shape/volume data operations.
(05 Oct 2005) Fixed bug in metric data deformation with tile areas.
(05 Oct 2005) Change toolbar's model selection control so that it when VOLUME is in it, it also lists the label/filename of the bottom most volume file.
(04 Oct 2005) Fix problem with Spec File Dialog buttons sometimes cutoff the bottom of the dialog.
(04 Oct 2005) Fixes for slices selection in volume oblique slice views.
(03 Oct 2005) Add import of MdPlot files.
(30 Sep 2005) Add node identification to montage volume views.
(30 Sep 2005) Fix centering of obliqe slices whose display is controlled by a transformation matrix.
(29 Sep 2005) Allow display of transform data files (cell/foci) even if the associated matrix's axes are not enabled for display.
(29 Sep 2005) Fix "Mutex" warning seen on MS Windows version of Caret when using the GNU compiler.
(29 Sep 2005) Add identification of transform data files (cell, foci) on oblique volume views.
(28 Sep 2005) Fix bug on transformation matrix dialog that turned the signs of all scale values to negative if the user just set one to negative.
(28 Sep 2005) Add display of transform data files (cells and foci) in volume oblique views.
(27 Sep 2005) Add montage for oblique slice views.
(27 Sep 2005) Now have only one Volume Oblique View Rotation Matrix. By default, the oblique slice views use the oblique view rotation matrix unless the user has selected a matrix from the transformation matrix file. Integrate oblique view matrix with the transformation matrix dialog. For oblique view slices, the slices in the toolbar are offsets from the oblique viewing slices.
(26 Sep 2005) Add 3D view to "ALL" view for oblique volume slices.
(23 Sep 2005) Add "ALL" view for oblique volume slices.
(22 Sep 2005) Add foci to oblique volume slice views.
(21 Sep 2005) Add oblique volume slice X, Y, and Z views. These slices are automatically yoked to the main windows Oblique View. An option on the Display Control's Overlay/Underlay - Volume's Settings panel allows the oblique slices to be yoked to a transformation matrix.
(19 Sep 2005) New Surface Vector File. Add a vectors submenu to the attributes menu. The only item on the Vectors submenu creates vectors based upon the difference between two loaded surfaces.
(15 Sep 2005) When drawing borders and assigning the nodes within the borders, allow the border assignment to operate when drawing 3D borders.
(15 Sep 2005) Add square root to mathematical operations on metric, shape, and volume data.
(13 Sep 2005) Fixed crash when a focus was identified with only a focus file was loaded and multiple fiducial surface files were loaded.
(13 Sep 2005) Fixed crash when an ID was performed in main window immediately after a viewing window was closed.
(13 Sep 2005) Remove use of size in cell/foci file when drawing cells/foci (see 12 Sep 2005).
(12 Sep 2005) If a voxel is indentified on a volume viewed obliquely, use the oblique rotation matrix to determine the voxels coordinates.
(12 Sep 2005) Allow the user to identify multiple nodes by having the user places spaces between the node numbers.
(12 Sep 2005) Use size from cell/foci file when drawing cells/foci.
(09 Sep 2005) Fix bug with selection of loaded volumes for volume to surface mapping.
(09 Sep 2005) Add operation to Surface Region Of Interest Dialog that automatically draws borders around clusters of selected nodes.
(08 Sep 2005) Add "ring" symbol for cells and foci. On Display Control Dialog, allow user to override the color file symbol for cells and foci.
(07 Sep 2005) Fix display of foci diamond symbols on flat surfaces.
(07 Sep 2005) Change surface to volume process by replacing "thickness" with an inner and outer boundary.
(07 Sep 2005) Add "Validate Spec File" to the File Menu. This queries the user for the name of a spec file and then verifies that the spec file and its data files exist. Copy Spec File and Zip Spec File now validate input spec file.
(06 Sep 2005) Surface Region of Interest Paint Subregion Report: Add center of gravity for regions X/Y/Z/Lat/Long coordinates.
(06 Sep 2005) Add item to file menu that "zips" a spec file and its data files. In addition, the same functionality is provided by the new command line program "caret_zip_spec".
(02 Sep 2005) Pressing on CTRL-Esc(ape) key combination on a window will pop up a file dialog for saving an image of the window.
(01 Sep 2005) Fix reading of MINC volumes whose data is not stored in an LPI orientation (zspace, yspace, xspace).
(31 August 2005) When drawing a border and assigning the nodes within the closed border to a new column, make the newly created paint column the selected paint column on the draw border dialog.
Change version to 5.31.
(31 August 2005) For brain models, separate view scaling into X, Y, and Z components.
(31 August 2005) Add some tooltips to the Transformation Matrix Editor Dialog.
(30 August 2005) Increase width of scale spin boxes on graph widget (used by SureFit operation's gray and white peak histogram panel).
(30 August 2005) Add button on Transformation Matrix Dialog to set the matrix's translation by clicking the mouse on a object.
(29 August 2005) Fix some problems with rotation of transformation matrix axes in screen space.
(10 August 2005) Add button to Map Stereotaxic Focus Dialog Studies panel for deleting the selected study.
(09 August 2005) Replace graph on the SureFit Segmentation Dialog with a new and improved graph for histogram display.
(09 August 2005) Correct histogram dialog on SureFit Segmentation Dialog so that is lists the actual voxel values and not the voxels scaled 0 to 255.
(09 August 2005) Add high (original) and low thresholding for removal of hindbrain during SureFit Segmentation.
(08 August 2005) Fixed crashing of SureFit Segmentation algorithm if the eye and/or hindbrain removal is skipped. Fixed auto-saving of surface files when inflated type surfaces are not generated.
(05 August 2005) Add additional attributes for color files: alpha channel and symbol type. Both alpha channel and symbol type are used by cells and foci. With additions to ColorFile, write the color files in XML format.
(04 August 2005) Add Cell and Foci Report that list attributes about cells/foci. In addition, paint information for the node nearest to each cell/focus may also be shown in the report.
(03 August 2005) Add mathematical operations to the command line program "caret_metric" used to modify metric files at the command line.
(02 August 2005) Fixed bug that failed to delete the intermediate files created during the deformation process.
(02 August 2005) Bug fix for surface deformation. If a data file failed to deform, the deformation immediately terminated and no more data files were deformed. Now, if a data file fails to deform, the deformation process stores the error message and continues with the deformation process. After the deformation process has completed, error messages involving problems with deformation of data files are displayed.
(02 August 2005) Add cells and foci for display on volume slices.
(01 August 2005) Attributes:Metric:Convert Metric Column to Functional Volume: Now have two options to interpolate (the existing functionality) or largest neighbor which sets the voxel to the larget metric value of the nodes that intersect the voxel.
(29 July 2005) Add "oblique" volume viewing. Include ability to yoke a surface in a viewing window to the volume for assisting with oblique volume orientation.
(28 July 2005) Draw Border Dialog: disable paint assignment if the 3D selection is set.
(28 July 2005) Edit Volume Attributes Dialog: add buttons for setting the Parameters File's AC or Whole Volume AC using the origin and voxel size.
(28 July 2005) Volume Resize Dialog: add option (defaulted on) for updating the Params File X/Y/Z min with the minimum cropping values.
(27 July 2005) If loading a cell/foci or cell/foci projection file and choosing to replace, delete cells/foci of all types.
(27 July 2005) Allow saving of cells for any surface type.
(27 July 2005) On reconstruct volume into Volume:Segmentation:Reconstruct Into Surface Dialog, add option to create a hypersmoothed surface.
(27 July 2005) Add new StereotaxicSpace class and use for all dealings with stereotaxic spaces.
(26 July 2005) Update Map Stereotaxic Focus Dialog that is split into two tabs for "Focus" and "Studies". Add additional GUI components for new foci data items. Also, add button for deleting the selected focus.
(25 July 2005) Add additional data to cell/foci files and cell/foci projection files all of which are now written in XML format.
(22 July 2005) Move common items from CellData class and CellProjection class into new parent class CellBase.
(21 July 2005) Allow user to set the random number generators seed value. If not set by user, default seed to the number of seconds since 1970.
(20 July 2005) When applying a transformation to a volume, allow the volume dimensions to grow so that the volume data does not get cropped.
(20 July 2005) Fixes/enhancements for volume transformations.
(20 July 2005) Fix but in new histogram dialog (14 July 2005) and add an Apply button for graph scale axes.
(20 July 2005) Fix colors for cuts during flattening of monkey brains but updating template borders with name of color file.
(20 July 2005) When a data file is saved with its name being changed, properly keep track of loaded files for scene creation and loading.
(19 July 2005) For entering foci, convert "em" or "en" dash characters (characters with varying length dashes, unicode charcters 8208 to 8213) to hyphens (minus signs).
(18 July 2005) Fix memory leak in VolumeFile operator=() that caused Caret to run out of memory during automatic error correction.
(18 July 2005) Fix up display of default gray/white peak histogram on SureFit Segmentation Dialog.
(18 July 2005) Consolidate histogram selection combo boxes scattered about into a single component.
(14 July 2005) Replace histogram dialog with a much improved version that allows complete control of the axes' scale and a grid background.
(13 July 2005) Change computation of standard deviation so that "N-1" is used for division in the formula. This implies that the true mean is unknown and that the data is a sample from the population.
(12 July 2005) Fix yoking so that if the surface is changed in a viewing window, yoking remains selected.
(12 July 2005) For surface shape cluster analysis on ROI dialog, warn user if no metric column is available for distortion correction.
(12 July 2005) Add "MFM" to multi-fiducial mapping statisitical measurement column names.
(12 July 2005) Fixed bug that caused a crash if a volume file was loaded and the metric cluster and smoothing dialog was displayed.
(11 July 2005) Fix bug in Surface: Region of Interest: Surface Shape Cluster Analysis. Any previously run cluster analyses are probably incorrect.
(07 July 2005) For Attributes Menu Compute Mean and Deviation on Metric/Shape, allow user to choose what should be computed and set the column names.
(07 July 2005) When switching from a flat surface with rotation axis set to OFF to a non-flat surface, default the rotation to XY.
(07 July 2005) Default Reference Column on Surface ROI: Surface Shape Correlation Report to ALL.
(06 July 2005) Change Attributes:Surface Shape:Subtract Group Average on Shape Files so that it operates on two surface shape files.
(06 July 2005) Fixed bug that occurred when the Surface Region of Interest Dialog was open and the number of metric, paint, or shape columns was reduced.
(06 July 2005) Add more text about shape file to Surface Region of Interest text report.
(06 July 2005) Add option on Attributes:Surface Shape menu to normalize all columns in a surface shape file.
(06 July 2005) For Attributes:Surface Shape: Compute T Map Shuffled Column, default coloring mapping to +/- 5.0.
(05 July 2005) Add fitting of metric or surface shape column data to a normal distribution.
(05 July 2005) Fix crash that happened when loading a topography file.
(01 July 2005) Add Vector Volumes which store a volume of vectors as a 4 component volume with the first three components being the unit vector and the last component being the magnitude.
(29 June 2005) Allow events to process during SureFit Error Correction.
(28 June 2005) For SureFit operations, if generating a segmentation and performing error correction, generate a surface from the initial segmentation and display it so that user can verify that there are no major problems such as the skull hanging around.
(28 June 2005) Fix near to planes in volume script builder.
(28 June 2005) Add surface shape cluster report to surface region of interest operations.
(27 June 2005) Fix 3D border drawing.
(27 June 2005) Correct application of a transformation matrix to a volume.
(26 June 2005) Add a few annotations to the Display Control Dialog.
(26 June 2005) Make dialog that shows errors encountered while checking all scenes non-modal.
(26 June 2005) Change warning message when unloading all files but scene and spec and there are modified data files.
(26 June 2005) Enable a vector file to be written as text.
(26 June 2005) When reporting foci stereotaxic position, always report the position on the active fiducial surface.
(26 June 2005) For scenes, retain the topology file assigned to each of the displayed surfaces.
(23 June 2005) Fix scene check bug for deleted surfaces still appearing to be present.
(23 June 2005) Add computation of Z-maps and T-maps for surface shape files.
(22 June 2005) Allow cells and foci drawn as sphere to have a size less than 1.0.
(21 June 2005) Set all volume coloring invalid when scene changed.
(21 June 2005) When checking scenes, verify that all needed files are in the Spec File.

NOTE: Remaining changes are listed from oldest to newest.

04 April 2004 - Release version 5.1

(12 April) Version changed to 5.11.
(12 April) Changed flat multi-resolution morphing parameters.
(12 April) Fixed spherical registration borders (dorsal medial wall, ventral medial wall, and calcarine) produced during full hemisphere flattening.
(12 April) Generate latitude longitude borders so that the north pole is at the lateral pole which is the tip of the Central Sulcus.
(12 April) Assign border colors after generating cartesian grid or lat/lon borders.
(12 April) If no paint or area color file was provided at start of flatten full hemisphere, the paint and area color file names ended up like "paint_file_#" and "color_file_#". Now uses topo file name to get a file name prefix for paint and area color files.
(12 April) If borders are loaded and border display is off, turn on display of borders.
(12 April) Add option to Save Data File Dialog to remove duplicate borders/border projections when saving a border or border projection file.
(12 April) Add menu item to rename a border by clicking on it with the mouse, which pops up a dialog allowing the border to be renamed.
(13 April) Remove some static data from node coloring.
(14 April) When performing multi-resolution morphing, only add the last coordinate file to the spec file. Other cycles are still saved, just not added to the spec file.
(14 April) Use meaningful names for spherical lat/long borders.
(14 April) Move unrecognized spec file tags to the spec file's header.
(14 April) Default border saving so that it removes duplicate borders.
(14 April) Spec File Dialog change to the remove from spec file "X" button next to each file. Now when the user presses the "X", the line is grayed out. If the user presses the "X" again, the line is re-enabled so that the file is not deleted. If a line is grayed out when the spec file dialog closes, the file is removed from the spec file.
(14 April) Add binary format for coordinate and topology files.
(15 April) Add binary format for areal estimation, lat/lon, metric, paint, rgb paint, section, and surface shape files.
(16 April) Replace current normals calculation that uses VTK because it is slow. Replace with normals calculation using coordinates and topology.
(16 April) Do not classify nodes after reading a spec file. Instead classify as needed such as when the primary overlay is set to Edges or the surface is drawn with Links-Edges only.
(16 April) Add utility program "caret_file_convert" to convert between binary and text (ascii) files.
(16 April) Add computation of average and deviation for each node in the surface shape file.
(19 April) Enable multi-threading for multi-resolution morphing.
(20 April) Add a copy button to the Identify dialog to copy the highlighted text to the clipboard.
(21 April) Update all projected files when surfaces are aligned.
(21 April) Add option to expand or shrink a surface along the surface normals to Surface: Geometry menu.
(21 April) Fixed bug that prevented fast open data file dialog close button from closing the dialog when the auto close checkbox was unchecked.
(21 April) Add a second light opposite of the existing light when drawing functional volume voxels so that they do not appear dark gray in the dorsal view.
(22 April) Add additional functional volume mapping algorithms for mapping functional data within Caret.
(26 April) Default to new column each time a functional volume is mapped within Caret.
(27 April) Do not allow spec file name to be changed in map_fmri_to_surface on the metric naming dialog.
(28 April) Created new program "caret_metric" for performing clustering and smoothing of metric files at the command line.
(29 April) Created deformation map file version 2. In this version, two new items are added, the source (individual) and target (atlas) directories. All of the source and target files are written relative to these directories. When applying a deformation map, the source and target directory names are verified to see if they exist. If not, the user must set them. This change simplifies the movement of a deformation to another computer system.
(29 April) map_fmri_to_surface so that it will display an error message if the atlas surface directory file (typically named "map_fmri_atlas.directory) version is 2 or greater. map_fmri_to_surface will be replaced with a program named "caret_map_fmri".
(29 April) Correct problem with every other frame being black when recording animation through volume slices.
(29 April) Fixed origin of AFNI volumes stored with R-A-S orientations. It was off by one voxel.
(30 April) Modify caret_file_convert to convert FreeSurfer Surface, Patch, Curvature, and Functional files to Caret format. Also convert VTK polydata.
(3 May) Rewrite some of caret_file_convert. Add BYU and STL file conversion.
(5 May) Add option on Display Control Dialog's border panel for adjusting the stretch factor when borders are draw as unstretched lines on a flat surface.
(5 May) Attributes: Lat/Long: Generate Lat/Long on Spherical Surface now assumes that the default view of the sphere is a dorsal view. Positive latititude is along the lateral axis and negative latitude is along the medial axis.
(7 May) Fixed problem with metric smoothing algorithm.
(7 May) Added Clustering and Smoothing for Surface Shape files.
(7 May) Fixed bug with caret_metric program crashing on Linux.
(11 May) Initial implementation of new fMRI mapper for individual and a surface loaded within Caret.
(11 May) Add "?" button for RGB paint on Display Control Dialog.
(11 May) Add display of surface shape information in the Identify Dialog.
(11 May) Add reference surface and surface used during distortion calculations to the surface shape column comments.
(11 May) Add the name of the surface used for curvature calculation to surface shape column comment.
(11 May) Fixed problems on histogram dialog when viewing middle 96%.
(11 May) Add button to set all columns to do not load when loading a node attribute file such as paint.
(11 May) Add option at Caret5 startup "-loadspec <spec-file-name>" that automatically loads the data files contained in "spec-file-name" into Caret. The option "-spec <spec-file-name>" simply loads the spec file "spec-file-name" into the spec file dialog.
(12 May) Added Mathematical Operations to Attributes: Metric and Attributes: Surface Shape. This allows two columns to be added, one column to be subtracted from another, one column to be divided by another, two columns to be multiplied, a column to be multiplied by a scalar, and a scalar added to a column.
(12 May) Add standard error for metric and shape average and standard deviation computation.
(12 May) Fixed some problems with probabilistic atlas coloring.
(12 May) Bug fix on D/C panel for prob atlas letting previous page show thru.
(12 May) Split metric clustering threshold into negative and positive.
(13 May) Now able to save (projected) foci associated with each surface type. However, only fiducial foci files are added to the spec file can Caret still only loads foci associated with the fiducial surface.
(14 May) Fixed cell/foci projection problem. When cells/foci project inside a tile, the offset of the cell or focus from the tile is saved as a vector in relation to the fiducial surface. The problem is that a cell or focus around the inferior part of the fiducial surface may have a vector with a negative z component. When this cell or focus is unprojected on the flat surface, it ends up under th