Commits on Nov 18, 2015
  1. error fixed

    And changes in preprocessing_AS file to make sure that it runs the
    advanced version of this motionparams function if it exists
    spopham committed Nov 18, 2015
Commits on Nov 11, 2015
  1. New motionparams file -- DRAFT

    Does extra manipulations with rotation differences across TRs to turn
    them into translational motion which is easier to interpret.  Needs
    more work though.
    spopham committed Nov 11, 2015
Commits on Nov 10, 2015
  1. Draft up file

    Still a work in progress
    spopham committed Nov 10, 2015
Commits on Nov 8, 2015
  1. very minor edit

    Stereo-Boy committed Nov 8, 2015
Commits on Nov 7, 2015
  1. Added more verbose and checks in white matter segmentation pipeline

    -I added comments and minor checks
    -I have also corrected minor display bug in mgz2niiIOrNoRS
    Stereo-Boy committed Nov 7, 2015
Commits on Nov 6, 2015
  1. correction of automated white matter segmentation and renaming

    I am testing right now so it may need more edits…(recon-all step is so
    Stereo-Boy committed Nov 6, 2015
  2. minor changes

    -rename ambiguous nu file to mprage
    -corrected some input trouble
    -does a beep when there is a pause/input so we can do something else at
    the same time
    Stereo-Boy committed Nov 6, 2015
  3. mostly file renaming

    -renamed automated_pipeline to preprocessing_AS
    -preprocessing_AS: added safety in case pathFile is not defined
    -preprocessing_AS: removed the useless alwaysGo
    -renamed sara’s ->
    -slightly edited preprocessing_AS to use *_SP files
    Stereo-Boy committed Nov 6, 2015
  4. Integrating itkGray processing dealing with correct orientations

    Set of different functions allowing to replace the too simple mgz2nii
    with the correct mgz2niiOrNoRS and other little stuff
    Stereo-Boy committed Nov 6, 2015
Commits on Nov 5, 2015
  1. New plotting file

    Required edits to adapt automated pipeline as well
    spopham committed Nov 5, 2015
Commits on Oct 30, 2015
  1. Updated pipeline automation files

    Mostly error catching and commenting
    Added mrGray options to white matter segmentation
    spopham committed Oct 30, 2015
Commits on Oct 29, 2015
  1. Minor comments

    Stereo-Boy committed Oct 29, 2015
Commits on Oct 28, 2015
  1. automated pipeline changes

    Changed to use new version of if available in
    zUsers/Sara (also on this commit)
    spopham committed Oct 28, 2015
  2. Alternative Motion Correction

    spopham committed Oct 28, 2015
Commits on Oct 27, 2015
Commits on Oct 25, 2015
  1. corrected bash profile bugs and cleaned

    Stereo-Boy committed Oct 25, 2015
Commits on Oct 21, 2015
Commits on Oct 20, 2015
  1. minor personal changes

    spopham committed Oct 20, 2015
Commits on Oct 16, 2015
  1. Corrected bash profile

    incorporates freesurfer path now
    Stereo-Boy committed Oct 16, 2015
Commits on Oct 15, 2015
  1. Solving the grow_gray matter issue

    and a little bug to allow correct nifti headers in a folder with other
    Stereo-Boy committed Oct 15, 2015
Commits on Oct 12, 2015
Commits on Oct 9, 2015
  1. corrected par file extraction for multiple predictor scenario

    minor modifications otherwise
    Stereo-Boy committed Oct 9, 2015
Commits on Oct 7, 2015
  1. Corrections for PAR files

    -PAR files are moved to correct folder (/Stimuli/Parfiles)
    -PAR files have colors
    -Added annotations/scangroup directly in mrVista session creation
    Stereo-Boy committed Oct 7, 2015
  2. Very minor

    Stereo-Boy committed Oct 7, 2015
Commits on Oct 6, 2015
  1. correct s_alignInPlaneToAnatomical file

    Stereo-Boy committed Oct 6, 2015
  2. Adding folder names

    spopham committed Oct 6, 2015
  3. merging with Sara

    Stereo-Boy committed Oct 6, 2015
  4. Update to make life easier for multiUsers

    -pathFile.mat will now store the personal folder paths for the auto
    -other files modified to work accordingly
    Stereo-Boy committed Oct 6, 2015
  5. Minor: corrected auto-pipeline with PAR files

    extractPARfile is a script to automatize PAR file creation (works only
    for stereo amblyopia project though)
    KatfMRIscript is the script made by Kat to combine motion correction
    parameters together
    Stereo-Boy committed Oct 6, 2015
  6. preprocessing edits

    My versions of automated preprocessing pipeline files.  Still a work in
    spopham committed Oct 6, 2015
Commits on Oct 2, 2015
  1. minor corrections

    -adding dateTime function
    -large corrections on nifitFixHeader2
    Stereo-Boy committed Oct 2, 2015
Commits on Sep 18, 2015
  1. Push #18: zUsers

    Stereo-Boy committed Sep 18, 2015
  2. Adding Adrien's package in Users

    This fixes the old pipeline 2015 on a Mac Yosemite / Windows 7
    It also uploads the automated pipeline draft and starts the zUsers
    Stereo-Boy committed Sep 18, 2015
Commits on Apr 3, 2013
  1. Merge pull request #17 from racheldenison/master

    Rachel's large pull request
    racheldenison committed Apr 3, 2013
Commits on Apr 2, 2013
  1. updated rd_centerOfMassGroupAnalysis to run when you give it a matrix…

    … of voxel sizes (which can be different for each subject) instead of a fixed voxel size for all subjects. with this change, the plots at various thresholds figure is now in units of voxels, insted of units of mm, as shown in the figure title
    Rachel Denison committed Apr 2, 2013