Caret:Documentation/ChangeLog

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Change Log

Caret 5 Changes

Version 5.64 (03 June 2011)

  • (03 June 2011) Patched file position bug in the QT Input/Output library that corrects the item identified on 17 March 2011.
  • (18 May 2011) Fixed crashes that occurred when a paint file contained indices larger than the index of the last paint name.
  • (17 March 2011) A bug is present in QT Version 4.7.1 QTextStream::pos() that corrupts reading of some Caret ASCII and Binary format data files. Caret is now able to detect the bug and inform the user of a way to work around the problem if it occurs.
  • (16 March 2011) Correct problem with cleanup of paint names.
  • (10 March 2011) Fixed (perhaps) problems with parameters containing spaces used in Command Executor and caret_command. On Mac, the script files that execute caret_command had to be changed to replace $* with "$@" to keep parameters from being split on spaces.
  • (08 March 2011) Fixed execution of caret_command launched through Caret's Command Executor.

Version 5.62 (25 Feb 2011)

  • (10 Feb 2011) Update the PALS coordinate files used to map volumes to surfaces to correct the coordinate system origin.

Version 5.616 (12 Nov 2010)

  • (12 Nov 2010) Add warning message to Ubuntu distribution of Caret (which we do not build that it contains reduced functionality and may not operate properly due to its use of incompatible versions of third-party libraries).
  • (12 Nov 2010) Fixed calculation of P-Values in statistical tests.; The index into the randomized clusters was off by one or two.
  • (11 Nov 2010) Changed cortical folding SI calculation to use atan2() instead of atan().
  • (16 Sep 2010) Updated caret file name regular expressions so that it supports new node number convention such as "164k_fs_LR".
  • (10 Sep 2010) Trying to fix problem with paint label editing that is apparently a problem with keeping GIFTI paint files and area colors synchronized.
  • (10 Sep 2010) Fixed failure of resample spec file command caused by 08 Sep change.
  • (08 Sep 2010) Fix create deformation map command for occurrance of both sphere not having the center of the sphere at the origin.
  • (30 Aug 2010) Fixed a bug in registration algorithms that was resampling each border many times (equal to number of points in the border).
  • (20 Aug 2010) Updated 711 volume origins.
  • (12 Aug 2010) Changed Volume Menu->Paint->Generate Colors for Paints Without Colors to also generate paint names for voxel indices that do not have a name.
  • (26 July 2010) Added the ability to read metric files in GIFTI format that contain two-dimensional MxN) arrays.  After the file is read,  N M-dimensional arrays replace the MxN array.
  • (01 July 2010) Added "caret-command -surface-border-file-merge" which merges border projection file.
  • (29 June 2010) Added "caret_command_test -surface-normals" which places a surface's normal vectors into a GIFTI vector file.
  • (28 June 2010) Added "caret_command -paint-label-name-update" which removes prefixes and suffixes from paint label names.  A suffix starts with the last period of the label name and a prefix ends with the first period in the label name.
  • (28 June 2010) Added "caret_command -paint-set-column-name" to set the names of column in paint files.
  • (25 June 2010) Curvature calculation was setting K1 to the principal curvature with the greatest absolute value.  K1is now the greatest value of the principal curvatures.
  • (18 June 2010) Added "Multi-Res Morph Parameters File" that stores the parameters used during multi-resolution morphing.  It can be loaded and saved in the GUI and added as an option to the command line multi-resolution morphing.
  • (18 June 2010) Added buttons to remove prefixes and suffixes from paint names to the Edit Paint Names dialog.
  • (14 June 2010) Fixed reading of GIFTI files with array order set to column-major order.
  • (26 May 2010) Changed caret_source/caret_qmake_include.pro. Any references to environment variables for includes or libraries were changed to add a second dollar symbol. This results in the VALUE of the environment variable being placed in the Makefile instead of the the environment variable itself. This eliminates the need to define environment variables in integrated development environments (Eclipse, XCode, etc).
  • (24 May 2010) Added surface area for each node to folding measurements metric file.
  • (20 May 2010) Added optional metric file output to folding measurments on Surface ROI Dialog and command line.  The metric file, on output, contains folding measurements at each node.
  • (26 April 2010) Fixed drawing of 3D symbols (unidirectional arrow/cylinder) for surface vectors when the vector's Z component was near zero.
  • (22 April 2010) Fixed reading of FreeSurfer binary format patch surface files.
  • (22 April 2010) After reading a Surface File, update the selected topology files.
  • (21 April 2010) Added an additional step to the operation that generates the cerebral hull volume from the segmentation volume.  In some cases with deep/large sulci, a small hole was present after the dilation operation and this hole was opened up during the erosion operation resulting in a "deep cave" in the cerebral hull volume and surface.  This has been corrected by filling any cavities that are present after the dilation operation but prior to the erosion operation.
  • (21 April 2010) Fixed help information for "caret_command -volume-erode" command.
  • (21 April 2010) Fixed "caret_command -volume-segmentation-to-cerebral-hull " which was mistakenly reading the hull volume as the segmentation volume. 
  • (14 April 2010) Fixed surface to segmentation volume conversion (caret_command -surface-to-segmentation-volume) that failed to sometimes work properly.  It turns out if the coordinate file was a left hemisphere and its structure tag in the header did not identify it as a left hemisphere, the code that filled the inside of the segmentation volume failed.
  • (14 April 2010) Added "caret_command -deformation-map-apply-generic-names" which applies a deformation map to a data file but allows the user to override the source and target files (coord/topo) contained in the deformation map file.
  • (13 April 2010) When reading a GIFTI file, check the type of the data arrays and convert them if necessary.  For example, a metric data file should have all of its data arrays at float data arrays and Paint file should have integer data arrays.
  • (30 March 2010) Remove all volume files prior to loading a scene.
  • (29 March 2010) Fixed reading of study metadata link from NIFTI volumes.
  • (09 March 2010) Fixed reading of GIFTI label files with colors included in the labels.
  • (05 March 2010) Display an error message if trying to import free surfer label files and none are found.
  • (05 March 2010) Fixed reading of column comments from gifti data array files.
  • (03 March 2010) Changed caret6 spec file conversion so that it ignores separate volume data files (*.img).
  • (01 March 2010) Fixed color assignment for paint files when paint file was read but lacked colors.  This fix is related to 01 Dec 2009 GIFTI label table update.
  • (22 Feb 2010) Changed Landmark-Vector-Difference spherical registartion so that when createing the source deformed coordinate file, it only flips the coordinates if it is the first cycle of the first stage when the source and target are different hemispheres.
  • (17 Feb 2010) Fixed scaling of surfaces to match the surface area of another surface.  Normally, this is run when creating inflated and other surfaces from the fiducial surface.
  • (10Feb 2010) Changed version to 5.614.
  • (10 Feb 2010) Fixed writing of NIFTI volumes with data type of signed 8-bit integer and the data value was greater than 127.
  • (10 Feb 2010) When converting a paint column to a paint volume, add all of the paint labels to the volume file, even those that are unused, so that the paint file and the paint volume use the same indices for the same label.
  • (10 Feb 2010) Added a new Caret extension to the NIFTI volume file.  Caret had used an extension of the AFNI extension but additional data did not fit well into the AFNI extension.  At this time, Caret still writes the AFNI extension so that the files will function with older versions of caret.
  • (09 Feb 2010) Rewrote cleanup of paint names to make it much faster.  This was needed because GIFTI files may have a few, large, sparse indexed labels which creates an enormouse label table with a million empty entries.  The alternative, rewriting the way labels are handled in Caret, is too ginormous of a change.
  • (26 Jan 2010) Changed version to 5.613.
  • (26 Jan 2010) Use a new set of deformation spheres for the Landmark Vector Difference deformation algorithm.
  • (25 Jan 2010) Fixed bug related to 18 Dec 2009.  When the corpus callosum volume was supplied as the anatomy volume the extent of the corpus callosum was not determined causing the medial wall border to fail.
  • (05 Jan 2010) Add endpoint factor for multistage vector deformation.
  • (05 Jan 2010) Fixed problems with border resmapling value on Deformation Dialog and proper saving to deformation map file.
  • (05 Jan 2010) Show variance when editing border file through Deformation Dialog.
  • (05 Jan 2010) When printing crossover message from Surface Vector Deformation, start at one instead of zero.
  • (05 Jan 2010) Fixed bug with last change that uses the remote ID for nodes so that when a scene is loaded, it does not try to display text for all of the nodes in the paint cluster auto loader region.
  • (04 Jan 2010) Show identification symbols over the paint cluster auto loader paint region.
  • (04 Jan 2010) Fixed problem with the metric palette colorbar failing to display when surfaces were displayed.

Version 5.615 (26 July 2010)

Change Log 2009

Change Log 2008

Change Log 2007

Change Log 2006

Change Log 2004

Change Log 2005

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