Caret 5 Changes

(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 the flat surface when it really should be above the flat surface due to the offset vectors negative z component. Now, the signed distance to the surface is combined with the surface's tile normal to properly offset the cell or focus when unprojecting.
(17 May) Default registration border resampling to 10.
(17 May) When deforming node attribute files, column names are prefixed with "deformed". File comments now include name of source file being deformed and the name of the deformation map file.
(18 May) Default probabilistic atlas to "normal" display.
(18 May) Add editing of surface shape column names to display control dialog.
(18 May) Fix editing of metric column names so that main display control page gets updated.
(19 May) Add option on save data file dialog to inhibit the automatic appending of a file type extension to the file's name.
(19 May) Add button to volume attributes editor dialog to use the params file AC to set the volume's origin.
(19 May) Add display of params file data in the "names" tab of the view data file comment dialog accessed by pushing the "?" button on the View Data Files or the Spec File dialogs.
(19 May) Add to Surface Region of Interest Dialog. New query that determines correlation coefficients between one column of surface shape and all other surface shape columns.
(20 May) Add item to Surface:Topology Menu to use vtkPolyDataNormals to consistently orient the triangles in the surface topology.
(21 May) Fixed error in metric and shape statistics that snuck in when standard error was added on 12 May.
(24 May) Add option to display a surface shape color bar in graphics windows.
(24 May) Do not require spec files when applying a deformation map to deform a data file.
(24 May) Add "deformed with" to columns when deforming a node attribute data file.
(24 May) Add check in spherical deformation for border files that are projected to nodes at origin.
(24 May) Add spin boxes to color selection dialogs.
(28 May) Add Layers:Borders:Create Average Borders to create average borders form border files that contain borders with the same names.
(1 Jun) Update Macaque flatten hemisphere template borders with http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=3370597.
(1 Jun) Use MIstart and MIstop parameters as origin and voxel size when importing minc volumes.
(2 Jun) Modify surface region of interest surface shape correlation report to enable correlation between all columns (creates NxN matrix).
(7 Jun) Add "version_id" to header each time a file is written. These version_id's will by used by SuMS to keep track of a files "heritage".
(10 Jun) In identify dialog, show coordinates for all open windows with surfaces displayed.
(10 Jun) Create a deformation field when a spherical deformation field is computed. This currently only compute the individual's deformation field.
(11 Jun) Add Generate Deformation Field to the Attributes Menu and display deformation fields as a layer controlled through the Display Control Dialog.
(14 Jun) Compute normals as first step when computing surface curvature.
(14 Jun) Add optional perspective projection.
(15 Jun) Reduced time to make surface cuts.
(22 Jun) Create atlas deformation field when performing a spherical registration or, post deformation, using the Attributes Menu.
(22 Jun) Add ability to deform coordinate files so that multiple cases may be loaded and viewed simultaneously in a single Caret session.
(23 Jun) Add information to Smoothing Dialog to inform the user that normals should be regenerated after smoothing a surface.
(23 Jun) Add Dialog to Surface Menu for averaging coordinate files.
(23 Jun) Add name of deformation map file to deformed coordinate file.
(24 Jun) Increase total number of model windows from 5 to 10.
(25 Jun) Fixed error that gave a paint file created during flattening of a full hemisphere an area color file extension. Add a check at the beginning of flattening a full hemisphere for a paint file.
(25 Jun) Limit update of version_id in spec file to once per caret session when saving data files.
(28 Jun) Add creation of topology file when deforming a flat coordinate file.
(28 Jun) Add warning when saving a volume in AFNI format and the file name does not end in an extension like "+tlrc.HEAD".
(30 Jun) Create binary version of deformation map file.
(30 Jun) Fixed bug with using a pre-loaded border file for template cuts when flattening a full hemisphere. Users must now use an ellipsoidal border file.
(1 Jul) Add Copy Spec File to File Menu for copying spec files.
(2 Jul) Added an interface to the SuMS database for downloading and uploading data sets. This is selectable from the Comm Menu.
(2 Jul) Add option (defaulted on) to the Flatten Hemisphere Dialog to smooth the medial wall of a fiducial surface during flattening of the full hemisphere.
(2 Jul) Add Convert Data Files Format to File Menu to convert data files between text and binary format.
(6 Jul) Trim leading and trailing whitespace when reading data file tag/value pairs.
(7 Jul) Implement surface editing (Surface:Edit menu).
(7 Jul) Possible fix for clipping problems seen in Surface & Volume mode. When optional perspective view was added, a call to gluLookAt() was also added but was being called for both perspective and orthographic viewing modes.
(7 Jul) Fixed crash after import of free surfer surface due to colors not being assigned.
(8 Jul) When uploading a spec file to SumsDB, strip the path from all of the data files listed in the spec file.
(8 Jul) Limit number of version_id updates to just one when a file is written out multiple times in a caret session.
(8 Jul) Add selection of previous data file directories on open, save, import, and export file selection dialogs.
(8 Jul) Clear file data file names on deformation dialog when a spec file is selected.
(9 Jul) No longer set version_id in file header when a data file is written. version_id will now be updated by SumsDB.
(9 Jul) Added volume borders.
(22 Jul) Implemented new functional volume to surface mapper. Removed "map_fmri_to_surface" from attributes:metric menu. "caret_map_fmri" is now command line only.
(22 Jul) Limit width of parameters (space, species, hem, etc) on spec file dialog so that all are visible even if data files have very long names making dialog very wide.
(23 Jul) Add quick mapping of a functional volume to an atlas surface to the Volume:Functional Menu.
(26 Jul) Fix crash if a coordinate file is read without any other files having been read.
(26 Jul) Limit width of previous spec files on choose spec file dialog.
(26 Jul) Limit width of previous directories on open and save data file, and import and export file dialogs.
(27 Jul) Added a spin box on the right side of the Identify Window to control the number of digits to the right of the decimal point in the data display window.
(27 Jul) Add "All On" and "All Off" buttons to surface region of interest attributes page.
(27 Jul) When reading a coord file, check its header for the topology file used by the coord file when the coord file was last saved, and, if that topology file is loaded, assign the topology file to the coord file's surface.
(27 Jul) Add brain model selection to the popup menu.
(27 Jul) Add menu item on Layers:Borders menu to convert volume borders into fiducial cells.
(28 Jul) Moved active fiducial surface (used in surface & volume and for overlay on volume) from Surface Information Dialog to Display Control Dialog's Surface Miscellaneous panel.
(28 Jul) Combo box at top of Display Control Dialog now only lists pages for data that is loaded.
(28 Jul) Holding down the CNTRL key (Apple on Macs) and pressing F1, F2, ..., F15 over a caret window will switch to the surfaces and volumes as listed in the toolbar's model selection menu.
(28 Jul) Store and use hem_flag in coord file header so that different hemispheres may be loaded simultaneously and toolbar buttons will work correctly.
(29 Jul) Add ability to set the maximum and minimum values for metric or surface shape on the metric/surface shape dialog.
(29 Jul) Add volume mathematics.
(29 Jul) Add optional output file parameter for "caret_metric" command line program.
(29 Jul) Add import of raw volume files.
(2 Aug) Add independent surface coloring that allows each surface to have its own surface coloring.
(2 Aug) Add ability to set hemisphere for a surface from the surface information dialog.
(3 Aug) Change independent surface coloring on display control dialog so that the control is available on all sub-pages that deal with surface attributes.
(3 Aug) Fixed "New Spec" button on spec file dialog so that it creates a spec file with all selected files.
(3 Aug) When using "New Spec" button and the user selects an existing spec file, give the user the opportunity to overwrite or cancel.
(5 Aug) Added display lists for surface drawing. Significantly improves performance on Macs.
(5 Aug) Fixed bug that voxels were not colored on surface and volume if a volume was not previously viewed.
(5 Aug) Add ability to draw segmentation volume voxels as filled, open squares, or crosses.
(6 Aug) Add ability to specify type of ouput file (binary or text) produced by the program "caret_metric".
(10 Aug) Add "caret_sphere_deform", a command line program for performing spherical registration.
(11 Aug) Add experimental smoothing that uses curvature and normals from an equation in a "level sets" paper. It can produce a surface similar to the inflated surface but with some high frequency spikes.
(13 Aug) Add graph that pops up when a node is identified, a metric is underlay or overlay, and popup graph is selected on metric panel of overlay underlay dialog.
(27 Aug) Fix bug that caused a blank image when the main window was saved as an image with display lists on.
(30 Aug) Add a "Simplify Surface" item to the Surface menu to reduce the number of polygons (and nodes) in a surface.
(31 Aug) When a volume file is read, default its sub-volume name to the name of the volume. If there is a sub-volume name in the volume file's header it will override the default name.
(31 Aug) Add segmentation volume editing - erosion and dilation.
(31 Aug) Default display lists off if the OpenGL library is a "Mesa" OpenGL library.
(1 Sep) Change "Finish" button on Map Fmri Dialog to "Map Data".
(1 Sep) On Map Fmri Dialog, only clear mapping surfaces if a volume is added or deleted. Previously, the mapping surfaces were removed when the volumes page was displayed.
(1 Sep) Remove Copy/Download Spec File page from Map Fmri Dialog.
(1 Sep) Modify Map Fmri Dialog so that average is created for each volume and multiple surface set.
(2 Sep) Modify Draw Border Dialog so that it checks for rotation when the Apply button is pressed on the Draw Border Dialog if a flat or compressed medial wall surface is being viewed. If there is a rotation, the warning will be displayed allowing the user to remove the rotation or ignore it.
(2 Sep) When processing the mouse allow no mouse movement or a very tiny mouse movement to preform and ID node operation when in View Mode.
(2 Sep) When computing metric/shape avg/dev/error, default the color mapping to the min and max values in the respective columns.
(2 Sep) Add segmentation volume editing flood fill and remove connected region.
(2 Sep) Add ability to set metrics or surface shape for nodes in an ROI.
(2 Sep) Modify color file editor to that when creating a new color, the name of the new color and its attributes are the same as the currently selected color.
(3 Sep) Add ability to adjust threshold for probabilistic atlas threshold display.
(3 Sep) Add new Attributes:Probabilistic Atlas menu item for converting a currently selected as overlay/underlay threshold probabilistic atlas to a paint column.
(3 Sep) Add hemisphere to parameters on file save dialog when saving a coordinate file.
(7 Sep) Modify volume animation. Now start on currently viewed slice. Have ability to set animate direction (positive or negative slice increment) and can set direction while paused.
(7 Sep) Fixed bug that caused a functional volume to be incorrectly colored when there was no metric file loaded. This probably resulted when independent surface coloring was added.
(8 Sep) Added Wu Region File that when used with a ROI volume (paint volume), a graph will popup when a node is identified that is in a selected ROI showing the timecourse for the region.
(9 Sep) Add dialog on attributes paint menu to map a paint volume into a paint file column.
(9 Sep) Changed code for updating GUI due to data file changes to allow for more than 32 files.
(9 Sep) Add import of SUMA's RGB file.
(10 Sep) fMRI mapper - change name to "AVERAGE - volume-name" and include names of coordinate files in the average column's comment.
(10 Sep) Add ability to set the column names for lat/lon file columns.
(10 Sep) Add ability to selectively read columns from a lat/lon file.
(10 Sep) Display lat lon column names in ID window.
(10 Sep) Modify Create Average Coordinate file so that a surface shape file containing the standard deviation for each node in relation to the surfaces it was averaged from.
(10 Sep) Add ability to use a surface shape column as a node position uncertainty that can be enabled on the Display Control Dialog's Surface Shape panel.
(13 Sep) Separate gaussian computation from Metric Mapping into it own class. Add gaussian smoothing to metric smoothing for both caret and command line metric smoothing.
(13 Sep) Add option on Open Data File dialog to indicate than an SPM2 volume is being read that has the right on the left.
(14 Sep) Modify spherical registration so that it deforms individual coordinate files to the atlas.
(15 Sep) Completed geodesic distance so that a path may now be displayed from the root node to the identified node. Geodesic data may now be saved to a geodesic distance file including multiple geodesic queries. Display of geodesic data is controlled on the Display Control's Geodesic panel.
(15 Sep) Add spherical coord files to the indiv coord files that will be deformed to the atlas when a spherical deformation is run.
(15 Sep) When a flat surface is selected for display, disable surface rotation. It may be re-enabled by selecting the rotation axis in the toolbar.
(20 Sep) Modify region graph to allow all time courses for display.
(21 Sep) Change spin box for Inflate Surface Dialog's inflation factor to step by 0.01 instead of 0.1.
(21 Sep) Add new palette file editor on Attributes:Palette Menu.
(22 Sep) Fixed problem with floating point spin box on surface inflation dialog by replacing floats with double in the floating point spin box widget.
(22 Sep) Misc changes to fMRI mapper.
(27 Sep) If edges only is display mode, do not allow selection of non-edge nodes.
(28 Sep) Do not put "Sub Volume" in volume file sub volume names.
(28 Sep) When a spec file is read, determing volume data files for any volume names that are specified with only the volume's header file.
(28 Sep) Update SuMS interface for host "sumsdb" instead of "brainmap".
(04 Oct) Make column names longer for metric, paint, shape on Display Control Dialog.
(04 Oct) Show beginning of names when Opening a Node Attribute Data file and choosing columns for loading.
(04 Oct) Add new Surface ROI - Statistical Report on Paint Subregions which performs a statistical report for each unique paint name in a selected paint column.
(04 Oct) Add option to Display Control Dialog to select a paint column which is checked for MEDIAL.WALL. If it has medial wall paint, and the option is enabled, the medial wall is colored overriding any and all overlay/underlay selections.
(8 Oct) Add path to spec file name when starting caret and loading a spec file (ie: caret5 -loadspec brain.spec) so that the spec file may be successfully opened using File:Recent Spec File.
(11 Oct) Separate OpenGL code from graphical user interface so that it can be used by WebCaret.
(11 Oct) Fixed problem with changing border color line size.
(11 Oct) Fixed bug with copying spec file that caused files to disappear if both the new and copied spec file were in the same directory.
(12 Oct) Create a default set of sections (1mm Y-axis) when a brain set is loaded that contains a fiducial surface.
(12 Oct) Fixed bug for display of sections (needed to delete display lists).
(12 Oct) Fixed bug for display of ROI highlighted nodes.
(12 Oct) Moved some code involving node display flags from BrainModelOpenGL to BrainSet and BrainSetNodeAttribute for better WebCaret compatibility.
(12 Oct) Fixed bug in Metric & Surface Shape file that was requesting way to much memory.
(13 Oct) Add gaussian smoothing for metric data that uses a spherical surface for some distance cutoffs. Updated caret_metric.
(13 Oct) Fixes for after contour and volume reconstruction.
(14 Oct) If a viewing window is open, show the name of its brain model in the window menu.
(14 Oct) Replace icon on standard dialogs with the caret icon.
(14 Oct) Fix text for metric color palette bar. Skip QFont code in BrainModelOpenGL for WebCaret.
(14 Oct) Add volume resampling by entering the desired voxel sizes.
(14 Oct) If a file is not found, prepend "(FILE NOT FOUND)" to its name on the spec file dialog.
(14 Oct) Add spherical retessellation on Surface:Topology menu when caret is started with the flag "-test".
(15 Oct) Add display of euler count on surface information dialog.
(15 Oct) Add SID button on Identify Dialog to inhibit the display of green symbols on the surface.
(15 Oct) Add display control of volume crosshairs to Display Control Dialog's Overlay/Underlay Volume page.
(15 Oct) Add anatomy volume thresholding (green above upper threshold, blue below lower threshold) to the Anatomy Histogram available on the Display Control Dialog's Overlay/Underlay Volume page.
(15 Oct) Fix import of SUMA RGB file with color components ranging 0.0 to 1.0.
(18 Oct) Add rotation to volume display and ability to apply the rotation to the displayed volumes. Also added ability to apply a transformation matrix volume files.
(18 Oct) Fix RGB coloring when it is the underlay to not allow anything to show through.
(18 Oct) Add continuous rotation to the Automatic Rotation dialog.
(20 Oct) Add Dialog for editing parameters file.
(29 Oct) Fixed crash that occurred if the Map Functional Volumes to Metric dialog was selected and at least one brain model other than a surface was loaded.
(29 Oct) Remove splash image and show surface after loading a spec file (bug fix).
(29 Oct) "Show Surface" pushbutton on Display Control's Surface and Volume panel had no effect when display lists were enabled (bug fix).
(01 Nov) After loading a volume file, do not check to see if all voxels are less than one and delay color assignment until the first volume is loaded.
(02 Nov) Only allow volume rotations when the "Rotation Enabled" item on the Volume:Transform menu is checked.
(02 Nov) Fix uploading of volume files so that the header AND the data are uploaded when only the header is selected.
(03 Nov) Fix crash if a spec file loaded with a coord file and no or invalid topology file.
(03 Nov) Restored lost functionality that displays a cross over the surface in other windows when a node is identified or a voxel is identified.
(03 Nov) Modify gaussian function so that it is now exp(x*x / 2*sigma*sigma). Previously "2" was not in denominator.
(16 Nov) Replace VolumeFile with a version that does not use VTK to store the volume data.
(16 Nov) Enable Map to Caret With Atlas when any surface is loaded and atlases are available.
(17 Nov) Add ability to segment an anatomical volume, produce a segmentation volume, and generate raw and fiducial surfaces.
(17 Nov) Improve 3D border drawing by determining the triangle under the cursor and using the barycentric position in the triangle to place the border point. Previously the border points were pulled to the nearest node.
(18 Nov) Allow update of comments in volume files on disk through the Open Data File dialog.
(18 Nov) Change "New Spec" button on Spec File Diaog to "Create New Spec" and warn user if choosing an existing spec file name.
(18 Nov) Fixes for Convert Data Files Dialog. Had two "Add Files" button and one of them should have been "Remove Files". Also remove all files when Close button is selected.
(18 Nov) When reading a segmentation volume assume any non-zero voxel is part of the segmentation and changes its value to 255.
(18 Nov) Add translucent display of segmentation volumes.
(19 Nov) Add ability to combine two paint volume files using Volume:Mathematical Operations Dialog and choosing to combine paint volumes.
(22 Nov) Add Probabilistic Atlas Analysis to Surface Region of Interest Dialog.
(22 Nov) Fix glitch with display of threshold probabilistic atlas.
(22 Nov) Add adjustable transparency for segmentation volume.
(22 Nov) Add ability to set name of output volume on volume mathematics dialog.
(22 Nov) Add ability to write volume brick files gzipped.
(22 Nov) Add ability to read/write paint volumes from/to AFNI volume files.
(23 Nov) Fix bug that caused part of the surface to be clipped at times. This would only happen after a volume had been viewed and the user switched back to viewing a surface. When a volume was drawn, it was overriding the near and far clipping planes.
(23 Nov) Speed up surface coloring by applying coloring from first surface to all other surfaces with the same color selections.
(24 Nov) Add ability to save all volumes of a specified type (anatomy, paint, etc) to a single multi-volume AFNI file.
(29 Nov) Fixed problem with deformed coordinate file being given hemisphere "unknown" which causes standard view buttons in toolbar to work incorrectly.
(29 Nov) Fixed bug with a program error being printed regarding an invalid display list when surface to volume conversions were performed. Solution was to create an "operator=()" for AbstractFile and prevent the display list number from being copied.
(29 Nov) Provide more information on Save Data File Dialog when saving an AFNI volume about proper file naming.
(29 Nov) Creating batch deformation file, omit file parameters that are blank.
(29 Nov) During flattening of a full hemisphere, while creating the landmarks for registration, remove the last link in the dorsal and ventral medial wall landmarks so that they do not overlap. If there is an overlap, it may cause crossovers during registration.
(29 Nov) Fixed reading of version 0 topography files.
(30 Nov) Added volume region of interest dialog with probabilistic paint analysis query.
(01 Dec) Additions to volume region of interest dialog. Added selection by segmentation volume, thresholded anatomy volume, and thresholded functional volume. Add segmentation and paint name center of gravity queries.
(01 Dec) Add Compress Front Face to the Surface: Geometry menu.
(01 Dec) Add button to save the contents of the histogram dialog to an image file.
(06 Dec) Fix combining paint volumes so that the output volume may be one of the input volumes.
(06 Dec) Change separator characters in region of interest reports to a semicolon instead of a tab.
(07 Dec) Display translucent uncertainty circles on the volume slices if a "Node ID Deviation" column of the Surface Shape file is enabled on the Display Control Dialog.
(07 Dec) Increase initial width of Idenfity Dialog so that all of toolbar is visable.
(08 Dec) Add subject to header of SpecFile and allow it to be set on the spec file dialog. If the species, subject, and hemisphere are valid, new file names will default to "species.subject.hem.file-type-name.date.num-nodes". "num-nodes" is only present for node attribute files.
(09 Dec) Add file extension to default file names.
(14 Dec) Fix default peaks on histogram dialog.
(14 Dec) Keep track of volume file type on Save Data File Dialog and Import File Dialog.
(14 Dec) Fixed problem with voxel crosshairs not jumping to identified voxel in volume display.
(14 Dec) When borders projected, make border projection file "modified".
(15 Dec) Update ".pro" files for FreeBSD O/S courtesy of Jason at MCW.
(15 Dec) Corrections for recently installed compress front face.
(15 Dec) Ignore nodes with names "GYRAL", "GYRUS", or "???" in threshold probabilistic node coloring.
(15 Dec) Display all paint volume names when a paint volume voxel is selected.
(16 Dec) Fix crash that occurred when a histogram dialog was displayed without peaks.
(16 Dec) Add labels and comments for sub-bricks in a volume. When a multi-volume file is read into Caret, each sub-brick is stored in its own "volume-file" in memory. Labels and comments can now be set for each of these using the "?" button on the view current files dialog or on the display control dialog's overlay/underlay - volume panel.
(16 Dec) Add item to file menu to set current directory.
(16 Dec) Add Text File Editor to File menu.
(20 Dec) Add probabilistic atlas volumes.
(20 Dec) Fix bug with handle finding crashing.
(20 Dec) Add item to Surface:Geometry menu to scale a sphere to the surface area of the fiducial surface.
(21 Dec) Add Layers:Compute Average Separation Between Border Point Pairs.
(21 Dec) Fix reading of an unusual AFNI volume whose Z origin was large and in Inferior-to-Superior orientation.
(22 Dec) Corrections/changes to volume probabilistic atlas normal coloring to make voxels darker if ??? (undefined) names are contributing to the voxel.
(22 Dec) Fixed bug with new output volume naming on the Volume Mathematics Dialog.
(22 Dec) Fixed bug that did not update Display Control Dialog probabilistic atlas volume panel when a probabilistic atlas volume was loaded after loading the spec file.
(22 Dec) Fix prob atlas threshold to paint conversion.
(22 Dec) Added Volume:Probabilistic Atlas:Convert Probabilistic Atlas to Functional which stores in the functional voxel the number of valid identifications for that voxel in all probabilistic atlas channels and areas that are enabled.
(23 Dec) Changed display of voxel data in the Identify Dialog. All functional, paint, prob atlas, rgb, and segmentation data is shown for the voxel.
(23 Dec) Fixed Import Data File dialog, had forgotten to add Prob Atlas Volume type.
(23 Dec) Fixed writing of volume data when the volume data originated as a byte with a scale factor. For now, Caret writes float volumes (unless RGB).
(27 Dec) Added palette coloring for surface shape.
(27 Dec) Added positive and negative minimum values for metric coloring. This allows greater control over palette colors to non-thresholded metric values.
(27 Dec) Use "*" to separate file name in preferences files since a space is a valid file name character.
(27 Dec) Add ability to set color and thickness for surface outline displayed over a volume slice.
(28 Dec) Add export to minc volume. When reading a minc volume use directional cosines for orientation.
(28 Dec) Add progress dialog to deformation.
(28 Dec) Print out paint names for which there are no area colors when assigning node colors.
(28 Dec) Improved 3D border drawing.
(29 Dec) When Display Control Dialog is launched, default to O/U - Volume page if there are volumes but no surfaces loaded.
(29 Dec) Change volume cropping stuff to that a volume may also be made larger (now "resize" instead of "crop").
(29 Dec) Enable Surface and Volume anytime an anatomical volume is loaded. A fiducial surface is no longer requried.
(29 Dec) Add display of segmentation volume cloud in Surface and Volume.
(30 Dec) Change point assignment within closed border to assume points have Z = 0.0.
(30 Dec) Add Padding of segmentation volumes.
(03 Jan 2005) Corrected problem with coord and topo files sometimes showing up as "(FILE NOT FOUND)" on the spec file dialog.
(03 Jan 2005) When deforming a node attribute data file (metric, paint, etc) make sure it has a sufficient number of nodes so that it will work with the deformation map file.
(03 Jan 2005) Add Remove Islands to Volume: Segmentation menu.
(05 Jan 2005) Changed Surface:Topology:Disconnect Islands to Remove Islands.
(05 Jan 2005) Added Topology Error Report to Surface:Topology menu. This performs a number of topological check to verify a surface is correct.
(05 Jan 2005) Add volume ROI paint percentage report.
(07 Jan 2005) Added Topology Error Report to Volume: Segmentation Volume. This approximately counts handles, cavities, objects.
(07 Jan 2005) Add generatation of cerebral hull volume to Volume: Segmentation menu.
(10 Jan 2005) Fix 30 Dec change so that only assume points have Z = 0.0 for border inclusion check if the non-negative only flag is false.
(14 Jan 2005) Fixed problems with SureFit segmentation algorithm so that the segmentation now matches that produced by the soon to be old SureFit program.
(14 Jan 2005) Add surface shape depth, surface shape curvature, and paint sulcal identification to the SureFit segmentation process.
(14 Jan 2005) Change Edit Volume Attributes Dialog so that it no longer requires that the volume whose attributes are being edited is in the main window. Instead, it warns the user, allowing the user to continue or cancel.
(14 Jan 2005) Add item to File menu to Close the current spec file (reset caret to its startup state).
(14 Jan 2005) Fix import of minc byte volume files to that 0 to 255 range is restored instead of being scaled 0 to 1.
(24 Jan 2005) Additional information added to Surface Topology Report Dialog.
(24 Jan 2005) Do not allow assignment of a topology file to a surface if the topology file references node numbers greater than the number of coordinates in the surface.
(25 Jan 2005) Add read and write support for NIFTI volume files. Caret can read a NIFTI file that it writes but no NIFTI files are available for testing at this time.
(25 Jan 2005) Fixed problem with upload of Volume File pairs (header and data) data file not receiving the proper parent ID when a spec file is uploaded.
(25 Jan 2005) When uploading files to SuMS make sure all of the files exist prior to starting the upload.
(26 Jan 2005) Modify data files for future support of XML reading and writing. Change SumsFileListFile, GenericXmlFile and CocomacConnectivityFile for new implementation of XML file reading.
(26 Jan 2005) Add keyboard commands for controling the view of brain models loaded in Caret.
(27 Jan 2005) Added ability to write a coordinate file in XML format with the coordinate data base64 encoded. This is just for experimentation purposes at this time.
(27 Jan 2005) Correct generation of lat/long for nodes with X=0. They were getting long = 0 but should have been +90 or -90.
(28 Jan 2005) Modify keyboard commands so that they use the same control/shift keys as the mouse.
(28 Jan 2005) Started adding a "transformation axis" that will be used to project objects not in surface space into the surface space.
(28 Jan 2005) Added a new drawing mode "tiles-links-nodes" designed for use with surface editing. It first draw the surface as lighted tiles using the current coloring. It then draws the links and nodes in blue.
(31 Jan 2005) Add option for metric/shape/volume math replace NaN with zero.
(31 Jan 2005) Fix problem with volume attribute operations when the volume is in the main window.
(2 Feb 2005) Update Mac OSX, Linux, and Windows version of Caret5 to use QT 3.3.4.
(2 Feb 2005) Fix errors in flat multi-resolution morphing caused by 24 Jan 2005 change that checked for topology file compatibility with coord files.
(2 Feb 2005) Add transformation matrices available to each loaded VTK model file.
(3 Feb 2005) Switch mouse mode between view and transformation axes when the axes are clicked with the mouse.
(3 Feb 2005) Modify rotation of transformation axes so that the mouse and keyboard controls rotate and pan in screen space.
(3 Feb 2005) With a surface or volume viewed, pressing the "m, l, d, v, a, p, r " keys switches to the default view medial, lateral, dorsal, ventral, anterior, posterior, and reset.
(4 Feb 2005) Now have thresholding separate for each column in a metric file. Thresholds are initially set while mapping functional volumes. Also, an option has been added to show below threshold nodes in green.
(7 Feb 2005) Corrections for spherical lat/long border generation.
(8 Feb 2005) New "average" threshold column for metric and set the average threshold during mapping of a functional volume.
(8 Feb 2005) Allow application of a transformation matrix to border, cell, foci, and vtk model files.
(8 Feb 2005) Add writing of VTK model files.
(9 Feb 2005) Change SuMS interface so that files are sorted by most recent date.
(9 Feb 2005) Modify transformation matrix dialog to get the matrix from displayed surface or transformation axes and transfer matrix to transformation axes view. Also load view for volume or surface and volume. Apply matrix to surface and volume.
(9 Feb 2005) Replace scale bar with axes that optionally show tickmarks and orientation labels.
(10 Feb 2005) Corrections for latitude and longitude +/-.
(10 Feb 2005) Combine the Map Functional Volume to Metric and the Map Paint Volume to Paint File into a single item on the Attributes Menu named Map Volume(s) to Surface(s).
(11 Feb 2005) Add volume montage display mode controlled on the Display Control Dialog's Overlay/Underlay - Volume panel.
(15 Feb 2005) Fix problem with an OpenGL error when selecting a transformation axis with the mouse.
(15 Feb 2005) Fixed appending of Transformation Matrix Files.
(17 Feb 2005) Add ability to view a transformation matrix as a set of coordinate axes.
(21 Feb 2005) Add Show Deformation Variability to Surface: Deformation menu.
(21 Feb 2005) Added FLIRT and MRITOTAL fmri mapping data files.
(21 Feb 2005) During deformation, set the configuration_id to flat or spherical for the resampled deformation borders.
(23 Feb 2005) Add info to project cells/foci dialog, that in most cases, the fiducial surface must be in an AC centered space.
(25 Feb 2005) Add ability to read some files (cells, foci, and vtk models) that are displayed in the space of a transformation matrix axes.
(3 Mar 2005) Correct origin for AFNI Talairach volume provided by VolumeFile.
(9 Mar 2005) Add initial implementation of automatic error correction to segmentation process.
(10 Mar 2005) Create some default matrices for AC to Native and Native to AC transformations.
(11 Mar 2005) Create a command line program "caret_volume" for performing operations on volumes at the command line. Current capabilities include thresholding and segmentation.
(14 Mar 2005) Remove spaces from surface type names in BrainModelSurface which fixes a bug for file names added to the spec file on MS Windows.
(14 Mar 2005) Fix date in default file naming for windows which was putting in the memory address instead of the date.
(14 Mar 2005) Add new dialog for creating the name of a spec file when the user chooses to create a spec file.
(14 Mar 2005) Fix problem with Compressed Medial Wall surface being upside down during flattening. I'm not sure what caused this but it may have been caused by some of the transformation changes made in February.
(14 Mar 2005) When a topology file is loaded, update topology selection on the surface ROI dialog.
(15 Mar 2005) On Flatten Hemisphere Dialog, try to automatically determine if the fiducial surface is AC-centered.
(15 Mar 2005) Add button to Volume Attributes Dialog to set a volume's origin using the Main Window Crosshairs as the Anterior Commissure location.
(16 Mar 2005) Add a scroll widget for contents of the Display Control Dialog due to its panels becoming too large for some monitors.
(16 Mar 2005) Add padding to partial hemisphere segmentation.
(17 Mar 2005) Add a check in flat deformation to ensure that both source and target have borders that begin with the name "LANDMARK", "landmark", "morph.", or "MORPH.". The flat_fluid program only uses borders with these extensions.
(21 Mar 2005) When generating a surface from a segmentation, remove any islands.
(21 Mar 2005) Put lots of C-library functions such as sqrt or atan in the std:: namespace which is required by the Borland C++ compiler for MS Windows.
(22 Mar 2005) Correct problem with volume cropping crosshairs sometimes incorrectly being shown.
(25 Mar 2005) If the only command line argument passed to Caret5 is a spec file, automatically load the Spec File into the Spec File Dialog. This allows Microsoft Windows User's to double click spec files to start Caret5.
(25 Mar 2005) When writing a Volume File, set the file type (AFNI, SPM, etc) based upon the header file's name's extension.
(25 Mar 2005) Fixed crash that occurred when Cancel button was pressed on Create Spec File Name Dialog.
(25 Mar 2005) Make sure there is surface coloring after the initial stage of flattening a full hemisphere.
(25 Mar 2005) Fix bug that occaisionally erroneously reported premature end of file when reading a Palette File.
(25 Mar 2005) Change a couple of float spin boxes on the Deformation - Flat Dialog to line edits due to a problem noticed only on Linux.
(25 Mar 2005) When reconstructing a volume to a surface, set the surface's orientation to the volume' s orientation.
(28 Mar 2005) Remove progress dialog when deformation exists due to an exception such as a missing file.
(28 Mar 2005) Hide volume to surface mapping dialog while operation is executing.
(28 Mar 2005) Pack items on various display control dialog pages to take up less space.
(28 Mar 2005) Identify Dialog: do not display voxel info when "V" is unselected, remove "N" node option, change "All" to "All-N" for all node information.
(30 Mar 2005) Rearranged some items on the Display Control Dialog's Overlay/Underlay pages for both surface and volume.
(31 Mar 2005) Add a "Deselect All" to the Spec File Dialog to deselect all files.
(31 Mar 2005) Change volume drawing so that there is only one threshold, not a min and max.
(31 Mar 2005) Embed a histogram dialog into the SureFit segmentation dialog to set the anatomy volume's gray and white matter peaks.
(31 Mar 2005) NOW VERSION 5.2.
(1 Apr 2005) Allow volume specified in spec file to be minc volumes.
(1 Apr 2005) If Open Data File Dialog is used to open a border file and there is no configuration_id in the border file, allow the user to specify the type of border file.
(4 April 2005) Add ability to delete the border projection file on the view current files dialog.
(4 April 2005) If the user tries to open a coordinate or topology file of an unknown type, ask the user for the type of the file.
(4 April 2005) When reconstructing a segmentation volume into a surface, a hole in the surface will result if any voxels in the edges slices are on. So, during reconstruction, pad the volume by one slice to prevent this problem.
(4 April 2005) Fix problem with column widths for metric and paint that occurred when the display control dialog was displayed prior to loading a metric or paint file.

06 April 2005 - Release Caret 5.2

(8 April 2005) Fixed independent surface coloring.
(13 April 2005) Initial implementation of scene which saves the state of overlays and underlays, windows open, window contents, and window positions. This data file is in XML format.
(13 April 2005) Mac users can now start Caret5 by double-clicking a spec file in the finder. Prior to double-clicking any spec file for the first time, the user must press the mouse once to select the and choose Get Info from Finder's File Menu. Click the menu below "Open with:" and select other and then find the Caret5 application.
(13 April 2005) Speed up node coloring when a surface has identical coloring as the first brain model.
(13 April 2005) Remove SureFit Crossover Check and set primary overlay to crossovers if any crossovers are found.
(13 April 2005) When using SureFit Segmentation Dialog to set the anatomy volume histogram, draw the thresholded regions in translucent green.
(13 April 2005) Do not require that voxel sizes be 1.0 in SureFit Segmentation.
(13 April 2005) Require voxel range in SureFit Segmentation to be [0, 255].
(14 April 2005) Add a multi-slice volume view that shows the horizontal, parasaggital, and coronal views in one window. This view is selected by selecting "All" from the volume slice control in the main or viewing window toolbar.
(14 April 2005) Change version to 5.201.
(14 April 2005) Added an option on the spec file dialog to select a transformation matrix. If a matrix is selected, the matrix will be applied to raw and fiducial border, cell, coord, foci, and volume files.
(15 April 2005) Add identification to volume slice ALL view.
(15 April 2005) Fix comment updater for XML files.
(15 April 2005) When saving scenes, always save highlighted nodes, properly use deformation field vectors, and always save surface shape.
(15 April 2005) Position Display Control and Identify Dialogs and Viewing Windows just off the Main Window.
(18 April 2005) Fixed setting of palette from a scene file.
(18 April 2005) Fixed widths of some sub-widgets on D/C Dialog.
(18 April 2005) Add Save As Image pushbutton to D/C Dialog.
(18 April 2005) Changes made to read newer CoCoMac files. On Open Data File Dialog, allow CoCoMac files to use ".xml" extension.
(18 April 2005) Add copy sub-volume to segmentation volume editing.
(18 April 2005) Add volume label to Save Data File Dialog.
(19 April 2005) Caret5 was crashing on a Windows XP system while "initializing data" during Spec File loading. OpenGL library vendor was listed as Intel. Installing Microsoft's software OpenGL libraries into Caret5's "bin" directory eliminated the problem.
(20 April 2005) Add ability to generate create a segmentation by just thresholding an anatomical volume.
(20 April 2005) When generating a surface from a segmentation volume allow the user to choose between generating a brain model surface or a vtk model file.
(20 April 2005) Add a segmentation voxel editing mode that allows the user to select a piece of segmentation and discard all segmentation voxels not connected to the selected voxel.
(21 April 2005) Add option on Display Control Dialog's Surface and Volume page to inhibit drawing of black voxels when volume slices are drawn.
(21 April 2005) Correct reading of VTK model files.
(21 April 2005) Add option to set volume coordinates using Params File's Whole Volume AC location.
(21 April 2005) Add default transformation matrices if AC Whole Volume parameters available.
(21 April 2005) Add identification of VTK model files.
(21 April 2005) Add scene saving for Surface and Volume parameters.
(22 April 2005) On MS Windows, sometimes received a "File is not writable" message. Code to check for file being writable has been disabled. May be a Samba issue (http://lists.trolltech.com/qt-interest/2004-01/thread00623-0.html).
(26 April 2005) Modify scene implementation so that it keeps track of all loaded files. If files needed for a scene are not in memory, Caret5 will automatically load them so that the scene is correctly displayed.
(26 April 2005) Add opacity for VTK model display.
(26 April 2005) Transformation Matrix Editor. When a new matrix is created, allow the user to choose the default values from an identity matrix, the current matrix, the current volume slices' stereotaxic coordinates, or the item at the center of the window when a surface is displayed.
(26 April 2005) Show axes letters (x, y, z) for transformation axes in volume view.
(27 April 2005) Modify saving of scene for transformation axes display.
(27 April 2005) Add Layers Menu items for converting borders, cells, and foci to VTK models.
(27 April 2005) Fix flickering hourglass during volume segmentation voxel editing.
(27 April 2005) Add scene replacement on Display Control Dialog's Scene page.
(27 April 2005) Changed copy spec file so that it always copies the scene file. This is necessary since the scene file contains paths that are typically relative to the spec file.
(27 April 2005) When user is saving a scene, warn user if there are any unsaved data files (except scene file).
(27 April 2005) Add a scene filter button on the Spec File Dialog toolbar.
(28 April 2005) Various changes for scene processing.
(28 April 2005) Fixes for one millimeter error in coordinates of WU NIL ifh volumes.
(28 April 2005) Show name of spec file on the View Current Files Dialog.
(28 April 2005) Add button on volume attributes to set the spacing and origin for a volume using standard stereotaxic space parameters. Only those spaces with matching dimensions are shown.
(28 April 2005) Update projected files when surface scaled or translated.
(29 April 2005) Update non-projected files (borders, foci, cells) when surface scaled or translated.
(29 April 2005) Add a voxel scaling operation to the Volume Attributes Dialog's Data page.
(29 April 2005) Made some fixes for scene operations with cocomac, prob atlas, and node IDs.
(3 May 2005) Add many more operations to the command line program "caret_ volume".
(4 May 2005) When reset button in toolbar is pressed, it is possible that the voxel with the (0, 0. 0) stereotaxic coordinate may be outside the volume. In this case, get as close to this voxel as possible.
(4 May 2005) Fixed drawing of volume borders.
(4 May 2005) Corrected label on Transformation Matrix Dialog for applying a transformation matrix to a volume.
(5 May 2005) Fix bug with volume border drawing.
(5 May 2005) Fix bug with applying volume rotation.
(5 May 2005) Initial implementation of volume operation script builder.
(9 May 2005) Fix some scene bugs: small jumps in window positions, deformation field never removed, surface outline color on volume slice, and surface shape palette selection.
(9 May 2005) Add image viewing windows selectable from the Window menu.
(10 May 2005) Fix display of scene files on Spec File Dialog when all files shown.
(10 May 2005) Incorporate image windows into scenes.
(11 May 2005) Made changes to correctly read WU-NIL ifh volume header files.
(11 May 2005) Add a Print Main Window item to the file menu to print an image of the main window. Note: printing does not seem to work on Windows versions of Caret5.
(11 May 2005) Add option to Volume Math Dialog to copy a volume.
(12 May 2005) On Spec File Dialog, if only volume files are shown, also show area colors files if there are any paint or prob atlas volumes listed.
(12 May 2005) When drawing borders on a volume, allow assignment of paint volume voxel within the closed border.
(12 May 2005) Add editing of paint volume voxels. Voxels are editing similar to segmentation voxels in that the mouse pointer functions as a paint brush.
(13 May 2005) Transformation Matrix Editor - when new matrix created, add option to set its values to the main windows view transformation matrix.
(13 May 2005) Scene fixes including failing to keep track of files that are loaded via the toolbar's "spec" button. Remove restrictions on names of scenes.
(13 May 2005) Fixed bug that was failing to unregister closed image windows that would cause Caret to crash at a later time.
(13 May 2005) Eliminate some messages about data files modified when saving or recreating a scene.
(16 May 2005) Draw surface outline over volume slices using triangles instead of links.
(16 May 2005) In metric comment for mapping functional volumes to surfaces, add the unit "mm" for neighbors in the comments.
(16 May 2005) Limit width of channel and area pages for probabilistic atlas on Display Control Dialog.
(16 May 2005) Correct update of active fiducial surface on Display Control Dialog's Surface Miscellaneous Page.
(16 May 2005) Save active fiducial surface to the scene file.
(16 May 2005) When mapping a volume to a multi-fiducial atlas, list the surfaces in alphabetical order.
(16 May 2005) When a coordinate file is saved, the topology file used by the coordinate file is placed into the header of the coordinate file. When loading the coordinate file and its cooresponding topo file is not loaded, automatically load the needed topo file.
(16 May 2005) Check for duplicate node attribute file column names when creating/replacing or showing a scene.
(17 May 2005) When mapping a volume to multiple surfaces, try to determine the case name and include case name in the metric data column name.
(17 May 2005) While uploading files to SuMS, hide the SuMS interface dialog.
(17 May 2005) Fixed bug that caused the "map to caret" buttons on the volume to surface mapper dialog to be incorrectly disabled.
(17 May 2005) Do not let the Animate or Histogram buttons on the Display Control's Metric page be the default button.
(17 May 2005) If a spec file is loaded and only scene files were selected, popup the Display Control Dialog and show its scene page.
(18 May 2005) Add option to determine the minimum and maximum columns when performing multi-fiducial mapping of functional volumes to surfaces.
(18 May 2005) When showing all 3 volume slices in a window, also show the fiducial surface.
(18 May 2005) When uploading a scene file to SuMS, strip the paths off any of the files listed in the SpecFile section of the SceneFile.
(19 May 2005) Add opacity for volume overlays.
(19 May 2005) Minor changes for items on map volume to surface dialog.
(19 May 2005) Add average for math operations on metric, shape, and volume files.
(20 May 2005) Add choice of color for identified node symbols on the Display Control Dialog's Surface Miscellaneous page.
(20 May 2005) Remove all model viewing windows when changing the scene.
(20 May 2005) Make entry of volume thresholds when mapping functional volumes optional.
(23 May 2005) Add an Image Editor to File Menu that allows viewing and editing (annotating, cropping, and resizing) of images.
(24 May 2005) Add item to Layers menu to copy the volume borders to the fiducial borders.
(24 May 2005) Add item to Volume Menu to create a new volume.
(24 May 2005) Add image opening and saving to image editing window.
(24 May 2005) Enhance the text file editor.
(25 May 2005) Fixed bug with replacing a scene. Now saves all settings, not just those for selected data types.
(25 May 2005) Fix crash caused by a color palette referencing a non-existant color.
(26 May 2005) Correct reading and writing of AFNI volume origins.
(26 May 2005) Add printing to image editor window.
(26 May 2005) Add printing to the text file editor.
(27 May 2005) Add some additional operations: find limits, intersect volume with surface, make plane, and pad volume to the caret_volume command line program. Updated script builder for these new commands.
(31 May 2005) When applying a transform to a volume use nearest neighbor interpolation for paint, prob atlas, segmenation, and rgb volumes and cubic interpolation for anatomical and functional volumes.
(31 May 2005) On Transformation Matrix Editor, correct loading of main window volume view transform.
(31 May 2005) Fix possible problem with current directory being altered when mapping a volume to a surface.
(31 May 2005) Allow specification of voxel data type when writing a volume file. Save Data File dialog only shows voxel data types that are valid for the type of volume file selected.
(1 June 2005) Corrected problem with mapping to multi-fiducial but only outputting the average.
(1 June 2005) When saving a volume file, warn user if the voxel values of the volume are outside the valid values for the selected data type.
(1 June 2005) Change display of images so that the center of the image is placed in the center of the main window.
(1 June 2005) Set the Z value of an image so that it is "far behind" the model in the main window.
(1 June 2005) Fix problem with main window resize handle not being on the right side of the status bar.
(2 June 2005) Add some more information to error message during deformation of a border projection file.
(2 June 2005) Add the program "caret_edit" for editing text files. This is just a stand alone version of the text file editor available on the File Menu. This simple text editor handles all of the different platform dependent line feeds.
(3 June 2005) Fixed bug with brain model viewing windows only showing up some of time when a scene was selected. The GUI system need to time to process its events so that it could close the windows when a scene was selected, prior to reopening the windows.
(6 Jun 2005) fMRI Mapping: average fiducial coord file now added to atlas spec files. Selection of average, deviation, etc. is now made each time a mapping atlas is selected.
(6 Jun 2005) When saving a gzipped volume, make sure ".gz" extension is on the data file's name in the spec file.
(6 June 2005) Add "Load Scene(s)" push button to Spec File Dialog. This will load all scene files and nothing else.
(7 June 2005) When loading node attribute file (metric, paint, etc) from Open Data File Dialog or Toolbar Spec button, if Erase All Columns is selected, switch the comment option to Replace.
(7 June 2005) Require at least an overlay or underlay volume for drawing borders on volumes.
(7 June 2005) When the viewed image in an image viewing window is changed by the user, preserve the view scaling.
(7 June 2005) Fixed deletion of surface shape file on view current files dialog.
(7 June 2005) On both Open and Save Data File Dialogs, corrected saving of previous directories (was one level too high) and update viewed files using selected filter when a previous directory is selected.
(7 June 2005) Add separate control for display of palette color bar on volume display.
(7 June 2005) Change version to 5.3.
(7 June 2005) If there is a selected deformation map file, make it the default deformation map on the Apply Deformation Map Dialog.
(7 June 2005) When showing a scene, avoid closing any model viewing windows that are needed by the new scene.
(7 June 2005) Fix crash that occurred when the Display Control Dialog was popped up for the first time after opening and closing a model viewing window.
(8 June 2005) Add more mathematical operations for metric, shape, and volume. New operations set a range of values (inclusive or exclusive) to zero.
(8 June 2005) Add slice thickness when drawing volume borders.
(8 June 2005) Default rotation for surfaes is now XY.
(8 June 2005) Fix so opacity for VTK models allows transformation axes to be seen.
(9 June 2005) Hide SuMS Database Dialog while files are downloading.
(9 June 2005) Add Identify Dialog to scenes.
(10 June 2005) Avoid scrolling list of scenes in Display Control Dialog when a scene is selected for viewing.
(13 June 2005) In the caret_volume program, disregard the debug on setting in the user's preferences file. When caret_volume is run from Caret's script builder and output from caret_volume is 8173 characters, caret_volume gets stuck writing I/O. caret_volume still works fine from the command line.
(13 June 2005) Fix size of model combo box on model viewing windows.
(13 June 2005) Make Display Control: Shape: Settings page wider so full name of palette may be seen.
(14 June 2005) Use full path to caret_volume program in volume script builder. Warn if the environment variable CARET_DEBUG is on since excessive output causes programs executed with QProcess to hang.
(14 June 2005) Fix command line switch for make sphere operation in caret_volume program.
(17 June 2005) Add scene insertion.
(17 June 2005) Print more information if Caret runs out of memory including an option to exit Caret.
(17 June 2005) Add option on Display Control Scene page to cycle through scenes and verify that they are valid.
(17 June 2005) Add ability to send scenes from one Caret application to another.
(20 June 2005) Various fixes for caret_volume command line program.
(20 June 2005) Fix Volume to Surface Mapper for Mapping Individual to Spec File.

20 June 2005 - Release Caret 5.3