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Fix regarding expected behavior of diff when finding image size #3

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Fix regarding expected behavior of diff when finding image size #3

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Commits on Aug 16, 2016

  1. indentation fix

    Noah C. Benson committed Aug 16, 2016
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  2. unified vocabulary

    Noah C. Benson committed Aug 16, 2016
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  3. Merge pull request vistalab#183 from noahbenson/master 

    Cleaned up the README.md and added Installation section
    @JWinawer
    JWinawer authored Aug 16, 2016
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  4. added a helpful error message if the system call to mri_convert fails

    Noah C. Benson committed Aug 16, 2016
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  5. added a helpful error message if the RdtClient function is not found

    noahbenson committed Aug 16, 2016
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  6. test script and function to update published tutorials

    @elinekupers
    elinekupers committed Aug 16, 2016
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  7. fix typo

    @elinekupers
    elinekupers committed Aug 16, 2016
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  8. add real tutorials to publish list

    @elinekupers
    elinekupers committed Aug 16, 2016
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Commits on Aug 17, 2016

  1. removed unneeded files from publishing tutorials

    @JWinawer
    JWinawer committed Aug 17, 2016
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  2. cleaned up ernie tutorials

    @JWinawer
    JWinawer committed Aug 17, 2016
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  3. new tutorial on slice timing

    @JWinawer
    JWinawer committed Aug 17, 2016
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  4. A tutorial for reading in/plotting the Benson et al. (2014) retinotop… 

    …y template of V1, V2, and V3
    noahbenson committed Aug 17, 2016
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  5. Merge pull request vistalab#184 from noahbenson/master 

    Added some helpful error messages
    @JWinawer
    JWinawer authored Aug 17, 2016
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  6. Fixed a minor bug in which a bash shell is launched non-interactively… 

    … to grab the FREESURFER_HOME or SUBJECTS_DIR when they are not set in the matlab environment; the shell is now launched interactively, so should always read the bash_profile
    noahbenson committed Aug 17, 2016
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  7. Fixed a typo

    noahbenson committed Aug 17, 2016
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  8. edited parameters

    noahbenson committed Aug 17, 2016
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  9. renamed to something more intuitive

    noahbenson committed Aug 17, 2016
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  10. Merge pull request vistalab#187 from noahbenson/master 

    Fixed a minor bug in which a bash shell is launched non-interactively…
    @JWinawer
    JWinawer authored Aug 17, 2016
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Commits on Aug 19, 2016

  1. Merge branch 'master' into nicrop

    @wandell
    wandell committed Aug 19, 2016
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Commits on Aug 20, 2016

  1. Comments and a little coding clarity on niftiView and niftiWrite 

    Reorganized the parameters and used inputParser for niftiAssignZeros.m
    @wandell
    wandell committed Aug 20, 2016
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  2. Added possibility of reading a .nii.gz file when only the base name i… 

    …s based. So, if you

pass in thisFile rather than thisFile.nii.gz we check for thisFile.nii.gz.  If it exists
we read it.  Otherwise we tell you that we couldn't find thisFile or thisFile.nii.gz.
    @wandell
    wandell committed Aug 20, 2016
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  3. Unnecessary file

    @wandell
    wandell committed Aug 20, 2016
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Commits on Aug 30, 2016

  1. Working on reading and writing tck files directly from disk into FG g… 

    …roup
    @francopestilli
    francopestilli committed Aug 30, 2016
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  2. ENH: Added direct load of MRTRIX streamlines from disk on file (from … 

    ….tck files0. Refactored fgRead.m using matlab fileparts to sort input.
    @francopestilli
    francopestilli committed Aug 30, 2016
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  3. ENH: removed parameters field from fgExtract.m might affect Quench be… 

    …havior.
    @francopestilli
    francopestilli committed Aug 30, 2016
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Commits on Sep 1, 2016

  1. ENH: fgExtract had some conflicts. Trying to resolve so to be abel to… 

    … make a Pull request to VISTASOFT/MASTER
    @francopestilli
    francopestilli committed Sep 1, 2016
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  2. Merge pull request vistalab#195 from vistalab/read_write_tck 

    Read write tck
    @francopestilli
    francopestilli authored Sep 1, 2016
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  3. Merge pull request vistalab#173 from vistalab/guimatlab2015 

    Add features for testing MATLAB2014b and later
    @francopestilli
    francopestilli authored Sep 1, 2016
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  4. Merge pull request vistalab#190 from vistalab/nicrop 

    Nicrop
    @wandell
    wandell authored Sep 1, 2016
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Commits on Sep 14, 2016

  1. new tutorial for making meshes from freesurfer

    @JWinawer
    JWinawer committed Sep 14, 2016
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  2. update freesurfer mesh tutorial to do visualization in matlab in addi… 

    …tion to mrMesh
    @JWinawer
    JWinawer committed Sep 14, 2016
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Commits on Sep 16, 2016

  1. Removed jsonlab

    @wandell
    wandell committed Sep 16, 2016
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Commits on Sep 17, 2016

  1. Fix minor bug: strcmp command checking that the file is a nifti file

    @rosemary-le
    rosemary-le committed Sep 17, 2016
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  2. Merge pull request vistalab#199 from rosemary-le/master 

    Fix minor bug: strcmp command checking that the file is a nifti file
    @rosemary-le
    rosemary-le authored Sep 17, 2016
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  3. Fix rmPlotCoverage to handle the case of plotting coverage of an ROI … 

    …with only one or two voxels (assumed median smoothing among other minor fixes)
    @rosemary-le
    rosemary-le committed Sep 17, 2016
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  4. Merge pull request vistalab#200 from rosemary-le/master 

    rmPlotCoverage edge case: ROI that is 1 or 2 voxels in size
    @rosemary-le
    rosemary-le authored Sep 17, 2016
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Commits on Sep 18, 2016

  1. Add feature to polarPlot.m and minor cleanup

    @rosemary-le
    rosemary-le committed Sep 18, 2016
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  2. Merge pull request vistalab#201 from rosemary-le/master 

    Add feature to polarPlot.m and minor cleanup
    @rosemary-le
    rosemary-le authored Sep 18, 2016
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Commits on Sep 19, 2016

  1. change in comments

    @JWinawer
    JWinawer committed Sep 19, 2016
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  2. cleaned up syntax

    @JWinawer
    JWinawer committed Sep 19, 2016
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  3. new average tseries tutorial, as well as updates to motion correction… 

    … tutorial
    @JWinawer
    JWinawer committed Sep 19, 2016
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Commits on Sep 26, 2016

  1. make mrvNewGraphWin consistent with newGraphWin by defining the globa… 

    …l variable GRAPHWIN and assiging it a value
    @JWinawer
    JWinawer committed Sep 26, 2016
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  2. Merge branch 'master' of https://github.com/vistalab/vistasoft

    @JWinawer
    JWinawer committed Sep 26, 2016
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  3. added ernie pRF tutorials

    @JWinawer
    JWinawer committed Sep 26, 2016
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Commits on Oct 12, 2016

  1. bug fix in converting freesurfer ribbon to nifti

    @JWinawer
    JWinawer committed Oct 12, 2016
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Commits on Oct 17, 2016

  1. Start of a method to convert fg data into tracts that can be visualiz… 

    …ed using the LORIS brainbrowser code. The format is Alias Wavefront OBJ, which is fairly general and can be visualized on macs/pcs using standard viewers, as well.
    @wandell
    wandell committed Oct 17, 2016
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  2. Edited comments at the head. Still stuff left to do. 

    We should get the documentation about MNI Obj files into the header of this file.
We should identify a data set to use for testing and put it in the Example section.
    @wandell
    wandell committed Oct 17, 2016
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  3. Added color parameter

    @wandell
    wandell committed Oct 17, 2016
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Commits on Oct 23, 2016

  1. Added comments to the header

    @wandell
    wandell committed Oct 23, 2016
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Commits on Oct 24, 2016

  1. Added ability for nitfiView to show one slice. 

    Shortened file name (which can be quite long) to first 10 letters of the name.
    @wandell
    wandell committed Oct 24, 2016
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  2. Minor comments and fixes

    @wandell
    wandell committed Oct 24, 2016
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Commits on Oct 25, 2016

  1. fg2MNIObj allows visualization of fiber tracts in a browser (for Flyw… 

    …heel)

Comments and small vixes for the dwiComputeSignal.m and other two files.  No code changes.
    @wandell
    wandell committed Oct 25, 2016
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Commits on Oct 26, 2016

  1. Comments in dwiGet/dwiPlot. Also returned estimated ADC in dwiPlot() … 

    …case.

Fixed the 'axis' required for identityLine.
    @wandell
    wandell committed Oct 26, 2016
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Commits on Oct 27, 2016

  1. Handling multiple coordinate cases properly for dwiQ and dwiGet. 

    Changed '.' to 'o' for my old eyes in dwiPlot(dwi,'adc' ...) case
    @wandell
    wandell committed Oct 27, 2016
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  2. Fix bug. Edge case when we bootstrap only once

    @rosemary-le
    rosemary-le committed Oct 27, 2016
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  3. Merge pull request vistalab#207 from rosemary-le/master 

    Fix bug. Edge case when we bootstrap only once
    @rosemary-le
    rosemary-le authored Oct 27, 2016
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Commits on Oct 28, 2016

  1. Added get a mean b=0 image 

    Added proper management for multiple coordinates in dwiComputeSignal
    @wandell
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  2. Merge branch 'master' of https://github.com/vistalab/vistasoft

    @wandell
    wandell committed Oct 28, 2016
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  3. Made symbols thicker

    @wandell
    wandell committed Oct 28, 2016
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Commits on Oct 31, 2016

  1. Removed the if statement that checked if fh = mrvNewGraphWin is a str… 

    …uct. The output of mrvNewGraphWin is a matlab.ui.Figure which behaves like a struct but is not a struct per se
    @rosemary-le
    rosemary-le committed Oct 31, 2016
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Commits on Nov 10, 2016

  1. Add niftiMerge.m, a function that takes in a list of niftis and retur… 

    …ns a nifti that is the logical union of all of them
    Rosemary Le committed Nov 10, 2016
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Commits on Nov 11, 2016

  1. Merge pull request vistalab#209 from rosemary-le/master 

    Removed the if statement that checked if fh = mrvNewGraphWin is a str…
    @rosemary-le
    rosemary-le authored Nov 11, 2016
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  2. Add isgraphics() to check the output of mrvNewGraphWin in the dtiChec… 

    …kMotion function
    Rosemary Le committed Nov 11, 2016
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Commits on Nov 13, 2016

  1. Add the option s0image back into dwiGet. s0image is synonymous with t… 

    …he b0image option and seems to have been inadvertently removed
    Rosemary Le committed Nov 13, 2016
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  2. Merge pull request vistalab#210 from rosemary-le/master 

    Add isgraphics() to check the output of mrvNewGraphWin
    @rosemary-le
    rosemary-le authored Nov 13, 2016
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Commits on Nov 15, 2016

  1. Updated the gifti reader. Still not working, though. Perhaps because … 

    …xmltree needs updating?

Also, need to fix t_gifti.m for new data model.
    @wandell
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Commits on Nov 16, 2016

  1. Added comments. No code changed

    @wandell
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Commits on Nov 18, 2016

  1. various bug fixes and new tutorial

    @JWinawer
    JWinawer committed Nov 18, 2016
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Commits on Nov 21, 2016

  1. Merge branch 'master' into jonTutorials

    @JWinawer
    JWinawer committed Nov 21, 2016
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Commits on Nov 30, 2016

  1. change fuction minmax to mrvMinmax to avoid conflict with matlab func… 

    …tion minmax in nnet toolbox. also change all calls to minmax to mrvMinmax
    @JWinawer
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  2. Merge branch 'master' into jonTutorials

    @JWinawer
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Commits on Dec 3, 2016

  1. Comments

    @wandell
    wandell committed Dec 3, 2016
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  2. Eliminate <OLD GLM> and <OLD Contrasts> from GLM menu bar

    @JWinawer
    JWinawer committed Dec 3, 2016
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  3. Merge branch 'master' of https://github.com/vistalab/vistasoft into j… 

    …onTutorials
    @JWinawer
    JWinawer committed Dec 3, 2016
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  4. replace dataDir with dFolder since dataDir is used as a variable but … 

    …is also a function
    @JWinawer
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  5. Eliminate <OLD GLM> and <OLD Contrasts> from GLM menu bar

    @JWinawer
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Commits on Dec 4, 2016

  1. Merge branch 'master' into jonTutorials

    @JWinawer
    JWinawer committed Dec 4, 2016
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  2. add compatibility to load niftis as parameter maps in gray view

    @JWinawer
    JWinawer committed Dec 4, 2016
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  3. bug fix for case when ROIs is a vector of integers

    @JWinawer
    JWinawer committed Dec 4, 2016
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  4. fix export of volumetric data as niftis

    @JWinawer
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  5. fix export of volumetric data as niftis

    @JWinawer
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  6. show colorbar for map view even range is undefined. otherwise we lose… 

    … the map name and units
    @JWinawer
    JWinawer committed Dec 4, 2016
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  7. tutorial update

    @JWinawer
    JWinawer committed Dec 4, 2016
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  8. tutorial update

    @JWinawer
    JWinawer committed Dec 4, 2016
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Commits on Dec 5, 2016

  1. revert

    @JWinawer
    JWinawer committed Dec 5, 2016
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  2. clean up tutorial

    @JWinawer
    JWinawer committed Dec 5, 2016
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  3. Merge pull request vistalab#214 from vistalab/jonTutorials 

    clean up tutorial
    @JWinawer
    JWinawer authored Dec 5, 2016
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Commits on Dec 29, 2016

  1. bug fixes

    @JWinawer
    JWinawer committed Dec 29, 2016
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Commits on Dec 30, 2016

  1. Updated to the newer (faster) jsonlab code. Supposed to be backwards … 

    …compatible.

Sure wish I had a test.
    @wandell
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  2. Continued update of jsonlab

    @wandell
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Commits on Jan 23, 2017

  1. clean up the figure windows at end of atlas tutorial

    @JWinawer
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  2. updates to get nifti datatype from niftiGet rather than writing it in… 

    …to a new field in the nifti struct
    @JWinawer
    JWinawer committed Jan 23, 2017
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Commits on Jan 24, 2017

  1. Change niftiWrite so that it is a wrapper to the mex file writeFileNifti

    @JWinawer
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  2. eliminate the call to add dataType field to niftiStruct. This value i… 

    …s now read from niftiGet
    @JWinawer
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Commits on Jan 28, 2017

  1. Merge pull request vistalab#218 from vistalab/nifti 

    Nifti
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Commits on Feb 3, 2017

  1. Return files in a cell array regarless of length.

    @lmperry
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Commits on Feb 17, 2017

  1. RF and BW jittering colors and converting to MNI OBJ format in the ne… 

    …wly edited code from Renzo.
    @wandell
    wandell committed Feb 17, 2017
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  2. fix jitter

    Renzo Frigato committed Feb 17, 2017
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Commits on Mar 1, 2017

  1. fixed the correction factor relating the computation of mean squared … 

    …error to sum of squared error
    @JWinawer
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Commits on Mar 3, 2017

  1. new validation test to ensure that nifti export works properly

    @JWinawer
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Commits on Mar 7, 2017

  1. First draft, not tested, of rendering multiple fiber groups as MNI OB… 

    …J files
    @wandell
    wandell committed Mar 7, 2017
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  2. Added subsample to make the file size reasonable for Flywheel

    @wandell
    wandell committed Mar 7, 2017
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Commits on Mar 8, 2017

  1. nice choice of 20 color samples. This routine will evolve

    @wandell
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  2. The fg2MNIObj now handles the fg array

    @wandell
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Commits on Mar 21, 2017

  1. use viewGet and viewSet rather than directly reading and writing to v… 

    …iew struct
    @JWinawer
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  2. exit without error if subject selects cancel in dialog box

    @JWinawer
    JWinawer committed Mar 21, 2017
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  3. account for possibilty that ROI name does not include .mat extension

    @JWinawer
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Commits on Mar 31, 2017

  1. remove obsoletedocstring

    Renzo Frigato committed Mar 31, 2017
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Commits on Apr 17, 2017

  1. Fix loadParameterMap.m so that the UI displays correctly when a nifti… 

    … file is chosen as a parameter map
    @rosemary-le
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  2. Merge pull request vistalab#225 from rosemary-le/master 

    UI did not get set to map mode when display a nifti file as a parameter map
    @JWinawer
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Commits on Apr 23, 2017

  1. minor change to comments

    @JWinawer
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  2. update to earlist level of Matlab supported, now up to 9.1.1

    @JWinawer
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Commits on Apr 24, 2017

  1. Added comments that specified ROI drawing options

    @rosemary-le
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  2. Merge pull request vistalab#228 from rosemary-le/master 

    Add comments to viewSetRoi.m
    @rosemary-le
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Commits on Apr 25, 2017

  1. Update README.md

    @JWinawer
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  2. ENH: Improved 3D figure handling. Fixed bug for which if 3D figure ha… 

    …d been closed the displaying woudl fail. A new figure is now created if necessary.
    @francopestilli
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Commits on Apr 26, 2017

  1. Changes that will compile readFileNifti default to requiring gz suppo… 

    …rt and be able to be compiled using mrvCompile.
    @j-ales
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  2. updated mex function for 64 bit mac readFileNifti

    @JWinawer
    JWinawer committed Apr 26, 2017
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  3. Merge branch 'readFileNiftiGzSupportFix' of https://github.com/vistal… 

    …ab/vistasoft
    @JWinawer
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Commits on Apr 27, 2017

  1. Added some comments explaining using options in mrvCompile

    @j-ales
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  2. changed the function call <display> to <disp> at Matlabs suggestion

    @JWinawer
    JWinawer committed Apr 27, 2017
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  3. minor syntax fixes

    @JWinawer
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  4. minor fixt to mrInit: make sure func.name is defined in the case that… 

    … no annotation text is provided for a scan
    @JWinawer
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  5. fix to viewGetVolume: when parameter classFile is called without a he… 

    …mi, assume left rather than returning an error. The logic is that class files are now generally NIFTIs, which are whole brain - neither left nor right, so it is reasonable to ask for the class file name without specifying the hemi
    @JWinawer
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  6. recompiled the mexmaci64 version of writeFileNifti for compatibility … 

    …with Matlab2017a. Also works with older versions, at least back to 2014b.
    @JWinawer
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  7. mrFlatMesh still needs this - can we make it a warning rather than di… 

    …sable completely?
    @wadelab
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  8. I think this was just a bug - the point of isfield is that you don't … 

    …have to access the field you are querying right?
    @wadelab
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  9. Slight tweaks to deal with matlab's stricter type checking on ui elem… 

    …ents. Also use setAnnotation in refreshView (rather than manually setting) and remove a call to MinColorMap property in openFlatWindow that doesn't seem to exist any more
    @wadelab
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Commits on Apr 28, 2017

  1. Comments corrected in niftiRead. 

    Recompiled myCinterp3 for Matlab 2017a on MacOs
    @wandell
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  2. Exit gracefully (issue a warning instead of an error message) when us… 

    …er changes mind about loading a ret model
    @rosemary-le
    rosemary-le committed Apr 28, 2017
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  3. Merge pull request vistalab#232 from rosemary-le/master 

    Exit gracefully when user changes mind about loading ret model
    @rosemary-le
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Commits on May 12, 2017

  1. dtiInit will now write out a scan to scan motion file

    @jyeatman
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Commits on May 16, 2017

  1. Merge pull request vistalab#234 from jyeatman/motioncheck 

    dtiInit will now write out a scan to scan motion file
    @jyeatman
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Commits on May 28, 2017

  1. dwiGet for adcdataimage needed to account for the case when there are… 

    … multiple b=0 images. In that case we use the mean b-0 image values. This was discovered while working on dtiError in scitranApps/dtiError.m

Added comments.
    @wandell
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  2. Comments mainly, though I added a small utility (wmCreate) to create … 

    …a lousy white matter mask from a nifti T1 data set. It is a hack that I need for now, when I don't want to depend on the user having FSL tools.
    @wandell
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Commits on Jun 9, 2017

  1. Added a new file to export fibers to MRTRIX format 

    This should create no conflicts with previous files.
    @francopestilli
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  2. Added option to save to disk a .tck (mrtrix) file. 

    This change should not affect the previous usage.
    @francopestilli
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Commits on Jun 13, 2017

  1. One function using nifti ROIs in endpoint to segment tract

    @htakemur
    htakemur committed Jun 13, 2017
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  2. Minor changes in variable names, and add more documentation

    @htakemur
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Commits on Jun 21, 2017

  1. freesurfer updates for compatibility with freesurfer 6

    @JWinawer
    JWinawer committed Jun 21, 2017
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  2. Made change for nearpoints to compile

    @wandell
    wandell committed Jun 21, 2017
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Commits on Jun 25, 2017

  1. Merge pull request vistalab#237 from vistalab/nifti_fg 

    Add one function using gray matter nifti ROI to segment white matter tract
    @htakemur
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Commits on Jun 29, 2017

  1. Update dtiExportFibersMrtrix.m

    @kitchell
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  2. Merge pull request vistalab#243 from kitchell/master 

    fix single quotes in dtiExportFibersMrtrix.m
    @francopestilli
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  3. update dtiExportFibersMrtrix 

     fix issues reading/writing header and other typos
    @kitchell
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Commits on Jul 11, 2017

  1. Merge pull request vistalab#244 from kitchell/patch-1 

    update dtiExportFibersMrtrix
    @francopestilli
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  2. ENH: Added option to pimport MRTrix fibers directly from the menu: Fi… 

    …le/Fibers Import
    @francopestilli
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Commits on Jul 12, 2017

  1. Robustness for .tck files with corrupted header 

    Often times the MRTRIX files (.tck) can have a header missing some information. I added a check for this and a warning.
    @francopestilli
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  2. Added option to save TrckVis format

    @francopestilli
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  3. Merge pull request vistalab#236 from vistalab/francopestilli-write-tck 

    Added option to save to disk a .tck (mrtrix) file.
    @francopestilli
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  4. Merge pull request vistalab#249 from vistalab/fgRead_TRK 

    Added option to save TrackVis format
    @francopestilli
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Commits on Jul 13, 2017

  1. updated mrtInstallSampleData to allow user to specify file type - pre… 

    …viously only zip allowed
    @JWinawer
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  2. update to code converting vAnatomy.dat to nifti, which was previously… 

    … failing
    @JWinawer
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  3. new test routine to ensure that conversion from vAnatomy.dat to nifti… 

    … is working
    @JWinawer
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  4. minor update: add HOMEDIR to path when loading tseries to avoid ambig… 

    …uous path
    @JWinawer
    JWinawer committed Jul 13, 2017
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  5. typos fiex in comments

    @JWinawer
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  6. fix to the way the max is computed when using the max method to map d… 

    …ata from the volume to the surface with multiple layers
    @JWinawer
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  7. merge with branch nojasonlab

    @JWinawer
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Commits on Jul 16, 2017

  1. Change to viewGet for case <mesh> - now, allows user to input optiona… 

    …l second argument to indicate which mesh, left or right
    @JWinawer
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  2. new function, meshImportFreesurferSurfaces, which grabs white, pial, … 

    …inflated, and sphere meshes from freesurfer, and saves them in vistasoft format. also updates to tutorials using meshes.
    @JWinawer
    JWinawer committed Jul 16, 2017
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  3. ensure tutorial runs even if user has not run previous ernie tutorials

    @JWinawer
    JWinawer committed Jul 16, 2017
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  4. new test function to check whether meshBuild, meshSmooth, and meshCol… 

    …or are working
    @JWinawer
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Commits on Jul 21, 2017

  1. fix to Ccode for nearpoints to compile successfully with both Matlab2… 

    …017a and Matlab2016b
    @JWinawer
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  2. Merge pull request vistalab#251 from vistalab/nearpoints 

    Nearpoints
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Commits on Jul 22, 2017

  1. All calls to waitbar have been replaced by mrvWaitbar. This is a new … 

    …wrapper function. If VISTA pref for VERBOSE is set to true, then mrvWaitbar calls waitbar and there is no difference in funtionality. If VERBOSE pref is false, then mrvWaitbar returns without opening a waitbar. This enables the user to easily prevent all popup waitbars.
    @JWinawer
    JWinawer committed Jul 22, 2017
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  2. Merge pull request vistalab#231 from vistalab/readFileNiftiGzSupportFix 

    Changes that will compile readFileNifti default to requiring gz suppo…
    @JWinawer
    JWinawer authored Jul 22, 2017
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  3. Revert "Changes that will compile readFileNifti default to requiring … 

    …gz suppo…"
    @JWinawer
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  4. Merge pull request vistalab#253 from vistalab/revert-231-readFileNift… 

    …iGzSupportFix

Revert "Changes that will compile readFileNifti default to requiring gz suppo…"
    @JWinawer
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  5. Revert "Revert "Changes that will compile readFileNifti default to re… 

    …quiring gz suppo…""
    @JWinawer
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  6. Merge pull request vistalab#254 from vistalab/revert-253-revert-231-r… 

    …eadFileNiftiGzSupportFix

Revert "Revert "Changes that will compile readFileNifti default to requiring gz suppo…""
    @JWinawer
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  7. Revert "Merge pull request vistalab#251 from vistalab/nearpoints" 

    This reverts commit fb46831, reversing
changes made to 7ab5fc4.
    @JWinawer
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  8. swithed test_exportNiftiParameterMap to use hidden inplane rather tha… 

    …n GUI
    @JWinawer
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  9. new test function for installing gray. also an update to cleanGray an… 

    …d cleanFlat that now creates backup of old gray and flat directories, rather than deleting them
    @JWinawer
    JWinawer committed Jul 22, 2017
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  10. Merge branch 'master' of https://github.com/vistalab/vistasoft

    @JWinawer
    JWinawer committed Jul 22, 2017
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  11. fix to new test function, test_installSegmentation.m

    @JWinawer
    JWinawer committed Jul 22, 2017
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  12. fix to nearpoints c code and mex file compiled for mexmaci64

    @JWinawer
    JWinawer committed Jul 22, 2017
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Commits on Jul 23, 2017

  1. new validation function to test mesh visualization

    @JWinawer
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Commits on Jul 25, 2017

  1. Merge pull request vistalab#252 from vistalab/waitbar 

    All calls to waitbar have been replaced by mrvWaitbar. This is a new …
    @JWinawer
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  2. for cleanGray and cleanVolume, first check whether folders exist befo… 

    …re trying to move and rename them
    @JWinawer
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  3. updates to fix the 4th column of the transform matrix of inplane nift… 

    …is, after transforming them from their native space to the preferred vistasoft space (PRS, or closest possible to that; see niftiCreateXform comments)
    @JWinawer
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Commits on Jul 28, 2017

  1. Merge pull request vistalab#256 from vistalab/fixInplaneXformMatrix 

    updates to fix the 4th column of the transform matrix of inplane nift…
    @JWinawer
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Commits on Jul 29, 2017

  1. Cast dims as mwSize rather than int in readFileNifti.c

    @JWinawer
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Commits on Jul 30, 2017

  1. updated versions of niftilib and newly compiled mex file for readFile… 

    …Nifti.mexmaci64
    @JWinawer
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Commits on Aug 8, 2017

  1. fixed a bug accidentally introduced a few months ago: <r> => <fileName>

    @JWinawer
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Commits on Aug 18, 2017

  1. Merge pull request vistalab#258 from vistalab/readFileNiftiFix 

    Read file nifti fix
    @JWinawer
    JWinawer authored Aug 18, 2017
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Commits on Sep 1, 2017

  1. variables <mn> and <sd> were used before being defined. that is now f… 

    …ixed
    @JWinawer
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Commits on Sep 21, 2017

  1. Trying support with a tricky back compatibility issue due to changes … 

    …to figure handles

ishandle is a function in 2014 so that should work

Jason D. Yeatman, PhD
Assistant Professor, Institute for Learning & Brain Sciences (I-LABS)
Department of Speech & Hearing Sciences
University of Washington
http://brainandeducation.com

On Wed, Sep 20, 2017 at 3:10 PM, Franco Pestilli <[email protected]>
wrote:

> But unfortunately, the current version of this function is incompatible
> with the current version of MatLab.
>
> Can ypu please test one of the following on your 2014b?
> ishandle(h1)
> isvalid(h1)
>
> Does any of these work for you?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <vistalab#241 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ABsYyjy178xZXLPFzOVoBGt_We73YuHkks5skY1lgaJpZM4OE-bu>
    @francopestilli
    francopestilli authored Sep 21, 2017
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Commits on Oct 5, 2017

  1. added the ability to compute a median of values along fiber groups ra… 

    …ther than a weighted mean
    jyeatman committed Oct 5, 2017
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  2. Merge branch 'master' into compmedian

    jyeatman committed Oct 5, 2017
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Commits on Nov 3, 2017

  1. Merge pull request vistalab#262 from jyeatman/compmedian 

    Compmedian
    @jyeatman
    jyeatman authored Nov 3, 2017
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Commits on Jan 10, 2018

  1. When loading a nifti file into a paramter map, treat the 4th dimensio… 

    …n as an index into the scannumber, rather than discarding all data beyond the 1st entry in the 4th dimension
    @JWinawer
    JWinawer committed Jan 10, 2018
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Commits on Jan 19, 2018

  1. minor formatting changes to various functions

    @rosemary-le
    rosemary-le committed Jan 19, 2018
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  2. Merge branch 'master' of https://github.com/vistalab/vistasoft

    @rosemary-le
    rosemary-le committed Jan 19, 2018
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Commits on Jan 20, 2018

  1. Add an additional case of predicting the rmTSeries for the css model

    @rosemary-le
    rosemary-le committed Jan 20, 2018
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Commits on Jan 23, 2018

  1. getTSeriesROI can take some time with large ROIs. Code now prints out… 

    … progress so user doesn't think the code crashed
    @rosemary-le
    rosemary-le committed Jan 23, 2018
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  2. rmPredictedTSeries works for the css model

    @rosemary-le
    rosemary-le committed Jan 23, 2018
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Commits on Jan 25, 2018

  1. updated most support to Matlab 9.2.1

    @JWinawer
    JWinawer committed Jan 25, 2018
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  2. new tutorial to show ROI usage

    @JWinawer
    JWinawer committed Jan 25, 2018
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  3. minor cleanup

    @JWinawer
    JWinawer committed Jan 25, 2018
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  4. minor cleanup

    @JWinawer
    JWinawer committed Jan 25, 2018
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  5. update to check4file to better handle non-.mat file types

    @JWinawer
    JWinawer committed Jan 25, 2018
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Commits on Feb 7, 2018

  1. append nifti file extension to output roi

    @lmperry
    lmperry committed Feb 7, 2018
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Commits on Feb 27, 2018

  1. allow for plotting single cycles when there are not an integer number… 

    … of time points per cycle
    @JWinawer
    JWinawer committed Feb 27, 2018
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Commits on Mar 7, 2018

  1. replaced <contains> with <strfind> since contains does not exist prio… 

    …r to Matlab 2017
    @JWinawer
    JWinawer committed Mar 7, 2018
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  2. replaced <view> with <vw> and various minor syntax updates

    @JWinawer
    JWinawer committed Mar 7, 2018
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  3. added support up to Matlab 9.3.1

    @JWinawer
    JWinawer committed Mar 7, 2018
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  4. added dataOverlay as optional output to meshColorOverlay

    @JWinawer
    JWinawer committed Mar 7, 2018
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  5. moved a line to avoid an error arising from calling a variable before… 

    … it was defined
    @JWinawer
    JWinawer committed Mar 7, 2018
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  6. removed dependency on view structure from the function to import free… 

    … surfer meshes
    @JWinawer
    JWinawer committed Mar 7, 2018
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Commits on Mar 8, 2018

  1. Update README.md

    @JWinawer
    JWinawer authored Mar 8, 2018
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Commits on Apr 3, 2018

  1. check whether VISTA preferences exist before calling getpref

    @JWinawer
    JWinawer committed Apr 3, 2018
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Commits on Apr 11, 2018

  1. Grab the exponent value first because effective sigma depends on the … 

    …exponent
    @rosemary-le
    rosemary-le committed Apr 11, 2018
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  2. add a colormap

    @rosemary-le
    rosemary-le committed Apr 11, 2018
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  3. Merge pull request vistalab#285 from rosemary-le/master 

    Minor changes to various functions
    @rosemary-le
    rosemary-le authored Apr 11, 2018
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  4. add an additional output to the rmCoordsGet.m function, to help keep … 

    …track of coordinates
    @rosemary-le
    rosemary-le committed Apr 11, 2018
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  5. add the css case for predicted tseries

    @rosemary-le
    rosemary-le committed Apr 11, 2018
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  6. Add a branch 

    Merge remote-tracking branch 'upstream/master' into crossModelValidation
    @rosemary-le
    rosemary-le committed Apr 11, 2018
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  7. Merge pull request vistalab#286 from rosemary-le/crossModelValidation 

    edits to rmPredictedTSeries.m
    @rosemary-le
    rosemary-le authored Apr 11, 2018
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Commits on Apr 12, 2018

  1. removed check for spm2 which uses function that breaks in 

    deployed(compiled) mode. vistalab#278
    @soichih
    soichih committed Apr 12, 2018
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Commits on Apr 19, 2018

  1. minor syntax updates

    @JWinawer
    JWinawer committed Apr 19, 2018
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Commits on Apr 20, 2018

  1. have the rmCoordsGet function return additional arguments pertaining … 

    …to the coordinates
    @rosemary-le
    rosemary-le committed Apr 20, 2018
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  2. Merge pull request vistalab#288 from rosemary-le/master 

    2 changes to rmCoordsGet
    @rosemary-le
    rosemary-le authored Apr 20, 2018
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  3. Fixed capitalization errors in rmSearchFit that was preventing ovals … 

    …from being fit
    @rosemary-le
    rosemary-le committed Apr 20, 2018
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  4. Merge pull request vistalab#289 from rosemary-le/master 

    Minor bugs in rmSearchFit that was preventing ovals from being fit
    @rosemary-le
    rosemary-le authored Apr 20, 2018
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Commits on May 18, 2018

  1. Update dtiImportFibersMrtrix.m 

    Original code expected one "counts:" field in a mrtrix .tck header.  This is problematic when using the mrtrix command cat_tracks to combine .tcks, which appends an additional "counts:" field to the end of the .tck header. Change is to just grab the max index and passing that through.
    bacaron authored May 18, 2018
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  2. Merge pull request vistalab#291 from bacaron/patch-2 

    Update dtiImportFibersMrtrix.m
    @francopestilli
    francopestilli authored May 18, 2018
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  3. added abs on false(sz) 

    use of false() as a means of getting an array of zeros on sz resulted in an empty dimension when a negative is passed in.  The previous structure seemed to be predicated on a presumption of either RAS or LPI.  Use of Abs(sz) ensures that the actual dimensions are passed.
    @DanNBullock
    DanNBullock authored May 18, 2018
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  4. Update dtiRoiToImg.m 

    per Dan Bullock (git user DanNBullock), use of false() as a means of getting an array of zeros on sz resulted in an empty dimension when a negative is passed in. The previous structure seemed to be predicated on a presumption of either RAS or LPI. Use of Abs(sz) ensures that the actual dimensions are passed.
    bacaron authored May 18, 2018
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Commits on May 22, 2018

  1. Merge pull request vistalab#287 from soichih/master 

    removed check for spm2 which uses function that breaks in deployed mode
    @wandell
    wandell authored May 22, 2018
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  2. Fixed as per Issue vistalab#293, roeysc

    @wandell
    wandell committed May 22, 2018
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Commits on May 28, 2018

  1. Merge pull request vistalab#292 from bacaron/patch-3 

    Update dtiRoiToImg.m
    @jyeatman
    jyeatman authored May 28, 2018
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Commits on Jun 29, 2018

  1. Comment formatting.

    @wandell
    wandell committed Jun 29, 2018
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Commits on Jun 30, 2018

  1. Quality of life utility. Need to add a Config routine

    @wandell
    wandell committed Jun 30, 2018
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Commits on Jul 3, 2018

  1. Some comments on the test related stuff. 

    Some updates on the gifti/OBJ stuff. This still needs work.
See comments about gifti and github and SPM12 in the files.
    @wandell
    wandell committed Jul 3, 2018
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  2. Comments

    @wandell
    wandell committed Jul 3, 2018
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Commits on Jul 5, 2018

  1. Moved the good stuff into the main t_gift.

    @wandell
    wandell committed Jul 5, 2018
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  2. Split t_gifti into simpler bits. Added information about how to downl… 

    …oad from RDT
    @wandell
    wandell committed Jul 5, 2018
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  3. Removed big file that was replaced by shorter versions

    @wandell
    wandell committed Jul 5, 2018
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  4. Data management

    @wandell
    wandell committed Jul 5, 2018
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Commits on Jul 13, 2018

  1. Retain full path when nii.gz extension is not provided

    @rokers
    rokers committed Jul 13, 2018
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  2. Merge branch 'master' of https://github.com/vistalab/vistasoft

    @rokers
    rokers committed Jul 13, 2018
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Commits on Sep 26, 2018

  1. Script for Silson et al. error

    @wandell
    wandell committed Sep 26, 2018
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  2. Comments and new validation routine

    @wandell
    wandell committed Sep 26, 2018
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Commits on Oct 3, 2018

  1. added live script <*.mlx* versions of several tutorials

    @JWinawer
    JWinawer committed Oct 3, 2018
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  2. minor: change in comments to fix file name in example

    @JWinawer
    JWinawer committed Oct 3, 2018
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  3. update of syntax, eg view->vw

    @JWinawer
    JWinawer committed Oct 3, 2018
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  4. added ./ to beginning of paths to avoid path ambuguity

    @JWinawer
    JWinawer committed Oct 3, 2018
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Commits on Oct 8, 2018

  1. added matlab live script versions of ernie tutorials

    @JWinawer
    JWinawer committed Oct 8, 2018
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Commits on Nov 26, 2018

  1. removed previous fix, added new one above 

    Per the comment in the main repo, the inability to deal with alternate orientations is leading to negative numbers here, which interacts poorly with the addition step.  (if the diff value ends up being negative, the addition of one reduces the actual size).
    @DanNBullock
    DanNBullock authored Nov 26, 2018
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Commits on Dec 10, 2018

  1. Merge branch 'master' into master

    @francopestilli
    francopestilli authored Dec 10, 2018
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