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Change Log 2009

  • (18 Dec 2009) If the input volume file name to auto-landmarks

contains "corpus" and "callosum" use it as the corpus callosum instead of extracting the corpus callosum from the anatomy volume.

  • (01 Dec 2009) Fixed crash that occurred when reading a FreeSurfer

binary patch file.  The patch file format seems to have been changed.  However, the new format is unknown so the best that can be done is to prevent the crash and display an error message.

  • (01 Dec 2009) Fixed writing of GIFTI Label file from Caret5 so

that the label table has its colors assigned (provided the area color file is loaded).

  • (01 Dec 2009) Added an "-area-color-file" option to

"caret_command -file-convert -area-color-file name.areacolor -format-convert" so that output GIFTI label files can receive colors.

  • (18 Nov 2009) Do not draw backfacing triangles when drawing foci

as 3D shapes.  Otherwise, if the foci opacity is less than one, the foci have a "half moon" appearance.

  • (16 Nov 2009) Save contour scaling in the contour file so that

scaling is preserved for any future contour drawing.

  • (13 Nov 2009) Draw surface foci before drawing the surface so

that the foci can be seen through a transparent surface.

  • (12 Nov 2009) Added a vector drawing mode that draws

unidirectional vectors without an arrowhead.

  • (05 Nov 2009) Fixed failure in automatic border drawing.  If

orbital sulcus is not found when creating the frontal cut, try to find the transverse orbital sulcus.  If neither are found, approximate a coordinate where the orbital sulcus should be.

  • (02 Nov 2009) Fixed dialog for setting the contour section

spacing.  It was always displaying the wrong value but the value entered by the user was properly processed.

  • (05 Oct 2009) Fixed bug with caret_command

-surface-foci-projection.  It was not properly processing the "-project-onto-surface" option.

  • (05 Oct 2009) Fixed bug with foci unprojection that occurred when

a focus projected to a node instead of a tile.  Fixing the problem required calculating the surface normal for the node since the tile normal was all zeros.

  • (28 Sep 2009) Fixed error that determined the structure of the

very inflated surface during probabilistic sulcal identification.  This bug was preventing the command line automatic border generation from functioning correctly.

  • (23 Sep 2009) Changed version

to 5.612.

  • (09 Sep 2009) Fixed quaternion parameter for NIFTI volumes with a

valid qform code.

  • (09 Sep 2009) Fixed use of structure in caret_command

-file-convert -sc.

  • (02 Sep 2009) Changed Vector Settings Functional Volume to use

the values as negative and positive thresholds.

  • (31 Aug 2009) Added cluster auto loaders to Connectivity Dialog.
  • (31 Aug 2009) Fixed crash that occurred if the user tried to map

foci to the PALS atlas with caret installed improperly so that the PALS atlas files cannot be found.

  • (31 Aug 2009) Fixes for paint dilation and metric/functional

volume auto loader crashes.   On the Display Control's Vector Settings page, keep the functional volume mask set to the last loaded functional volume if the selected functional volume becomes invalid.

  • (25 Aug 2009) Added functional volume masking to Display

Control's Vector Settings page.

  • (25 Aug 2009) Added "caret_command -paint-dilation" which dilates


  • (24 Aug 2009) Added "caret_command -surface-border-to-paint"

which assigns border names to nodes that are nearest to a link in the border.

  • (24 Aug 2009) Implemented limit of vector display to those within

an angle of an orthogonal axis.

  • (24 Aug 2009) Functional volume auto loader and multiple metric

auto loaders now working and working with scenes.

  • (21 Aug 2009) Metric auto loaders now work with scenes. 

Changed some default settings for the Display Control's vector settings page.

  • (19 Aug 2009) On Display Control's Metric Setting's page, add

Auto Scale - Percentage.  This new mode maps the metric values to percentages of the min/max positive/negative values.

  • (19 Aug 2009) Moved metric auto loading (4 metric auto loaders)

from Display Control to the new Connectivity Dialog.  The dialog is launched using the Attributes->Connectivity menu item.

  • (18 Aug 2009) Metric auto loading is now triggered by clicking on

a volume slice or in Surface & Volume surface and slices.s

  • (14 Aug 2009) Fixed reading of a volume border file using File

Menu->Open Data File.

  • (14 Aug 2009) Fixed writing of AFNI headers so that coordinates

and spacing are always the weird RAI even though the data is LPI.

  • (10 Aug 2009) Print additional information if surface

registration failed due to a problem with a landmark border file.

  • (04 Aug 2009) Changed effect of surface clipping on

vectors.  Vectors are displayed when there origin (arrows) or center (oriented) is within the clipping planes.  The clipping planes no longer remove parts of vectors.  Each vector file is now maintained separately in memory and the display of each vector file is controlled on the Display Control's Vector Selection page.  Fixed update of the segmentation volume selection control on the Vector Settings page.

  • (30 July 2009) Fixed reading of GIFTI files with data stored in

an external file and data arrays without a "data" tag.

  • (29 July 2009) Vector Changes: Reduced number of polygons used to

draw cylinders and cones.  Split vector volume slice thickness into distance above and below the slice.  Added magnitude threshold to Display Control's Vector Settings page.  Added a coloring mode that draws using the colors assigned to the vector or applies the vector's XYZ-unit vector as a red, green, and blue color components.  Add optional use of segmentation volume that is used as a mask to limit the display of vectors.

  • (28 July 2009) Renamed "caret_command -volume-to-vector" to

"caret_command -volume-fsl-to-vector".  It now requires a volume in the output space and correctly builds and applies the FSL transform so that the resulting vectors are in the output space.  An option allows the user to save the created transformation matrix.

  • (27 July 2009) Added Surface line width and volume slice

thickness to the Display Control's Surface Vector page.

  • (27 July 2009) Changed reading of NIFTI volume file header data.
  • (16 July 2009) Added new surface drawing modes for vectors that

draw the vectors as lines.  This is needed because the 3D arrows and cylinders can take a long time to draw, especially if there are many of them.

  • (16 July 2009) Added new Surface Clipping page to the Display

Control.  Surface clipping allows one to inhibit the display of a surface and its data for all six axis (negative and positive X, Y, and Z).  Partial View was removed from the Surface Miscellaneous page since Surface Clipping can provide the same functionality.

  • (15 July 2009) Incorporated Tim's automatic landmark

identification updates.

  • (15 July 2009) Replaced the surface vector file with VectorFile

which is in GIFTI format.  Replace Display Control's Surface Vector Settings page with Vector Settings Page.  Eliminated Display Control's Surface Vector Selection page.  The new vectors are displayed on both surfaces and volumes.

  • (15 July 2009) Added "caret_command -volume-to-vector" which

converts vector data, produced by BEDPOST and stored in volume files, into VectorFiles.

  • (08 July 2009) Renamed the "VectorFile" used only during SureFit

operations to "SureFitVectorFile".

  • (07 July 2009) Fixed problem with the preferences file being

written to the current directory instead of the user's home directory.  This error only occurred if the user did not have an existing preferences file in his/her home directory.

  • (06 July 2009) Fixed error caused by printing help information

for the command "caret_command -surface-border-landmark-identification".

  • (02 July 2009) Added "caret_command -spec-file-change-resolution"

which changes the resolution of surface data files in a spec file.

  • (01 July 2009) Fixed linking of cell and foci projection files

when deforming data files.

  • (29 June 2009) Have "caret_command -volume-euler-count" exit with

a message indicating that "-volume-topology-report" should be used instead.

  • (23 June 2009) Added a second metric auto loader to the Display

Control's Metric Settings page.

  • (22 June 2009) Add text to the "out of memory" message that

indicates non-English character sets may be the cause of the problem.

  • (18 June 2009) Made fixes to landmark vector surface-based

registration algorithm.

  • (18 June 2009) Print an error message if a named matrix does not

exist when "caret_command -surface-apply-transformation-matrix" is run.

  • (15 June 2009) Added dilation mode of metric smoothing.
  • (15 June 2009) Updates and fixes made to the Surface Deformation


  • (12 June 2009) Added "caret_command -surface-border-to-metric"

command that transfers the border's variance to nodes used by the border.

  • (12 June 2009) Modified Spherical Deformation Dialog for the

spherical vector algorithm.

  • (27 May 2009) Fixed export of Free Surfer Label files from caret5.
  • (19 May 2009) Fixed crash that occurred when trying to smooth a

spherical surface using the GUI.

  • (13 May 2009) For coordinate difference, allow the XYZ component

differences to be absolute value or signed.

  • (08 May 2009) Report crossovers during any cycle of spherical

deformation.  Save source and target borders at beginning of each cycle.

  • (08 May 2009) Add previous directories list to the file dialog

for selecting a deformation map file on the spherical deformation dialog.

  • (08 May 2009) Change the surface deformation dialog so that it is


  • (07 May 2009) Display Control:Surface Miscellaneous Page:Link

Size now affects "Links (No Backside) drawing mode.

  • (28 April 2009) Fixed bug that caused border line width to affect

the link size in surface links no backside drawing.

  • (28 April 2009) Add names of deformation map files to Deformation

page of Flat/Spherical Deformation Dialog.

  • (27 April 2009) When running spherical deformation through the

GUI and there is a surface in the main window at the time deformation is run, see that any surface displayed during spherical deformation are displayed in the same orientation as the surface that was originally in the main window.

  • (10 April 2009) Correct writing of NIFTI volume QFORM information

so that QFORM is correct when read by programs that choose QFORM over SFORM.

  • (10 April 2009) Modified the Apply Current View code so that it

no longer uses OpenGL subroutines for matrix computations.  As a result, the compressed medial wall surface can now be generated on the command line.

  • (08 April 2009) For "caret_command -surface-generate-inflated",

disable the compressed medial wall option since it will not work on the command line due to its usage of an OpenGL method for rotation.

  • (03 April 2009) Fixed display of foci linked to table with a

blank table subheader.

  • (01 April 2009) Fixed a crash caused by two nodes have an

identical coordinate during surface morphing.  Also, tests for NaN where added if debugging is on.

  • (30 Mar 2009) Fixed problem with reading GIFTI data files that

caused the file's metadata to be missing.  This problem was discovered when foci were not projecting due to the surface's structure being invalid.

  • (04 Feb 2009) Fixed crash that occurred if the last column of a

node attribute file was deleted using the Manage Loaded Files Dialog.

  • (29 Jan 2009) Changed version to 5.611.
  • (29 Jan 2009) Removed the "8081" sums host from the SumsDB dialog.
  • (27 Jan 2009) Fix excessive pop-ups of the L-to-L, R-to-R warning

such as when scenes are displayed.

  • (27 Jan 2009) Modify foci study validation to check that a focus'

class name matches either the linked table subheader short name, figure panel task description, or page reference subheader short name.

  • (27 Jan 2009) Added "caret_command

-surface-foci-reassign-study-names" to set foci names to study names.

  • (09 Jan 2009) Add an option to the Surface Region of Interest

Dialog that allows limiting the ROI to a three-dimensional region.

  • (09 Jan 2009) Add message that pops up when a "Left-toLeft,

Right-to-Right" selection is made on the display control.

  • (09 Jan 2009) Added "caret_command


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