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Shell C Matlab Python Batchfile Awk
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DeDriftAndResample *Same changes for DeDriftAndResamplePipeline and some bug fixes Jan 11, 2017
DiffusionPreprocessing Removed attempted support for a mulit-token value for the --printcom=… Oct 26, 2016
Examples *PostFIX edits to enable working with FIXMultiRun Jan 16, 2017
FreeSurfer Added cleanup code supplied by Mike Harms to FreeSurferHighResPial.sh Apr 12, 2016
GenerateSpinEchoBiasFieldPrereqs Removed attempted support for a mulit-token value for the --printcom=… Oct 26, 2016
ICAFIX created version of hcp_fix for use with FIX 1.06a (separate from vers… Jun 3, 2016
MSMAll Got all Matlab code to compile under Matlab R2013a on my workstation Jan 12, 2017
MSMBinaries *Add MSMSulc (currently untested) and some other minor changes Jan 16, 2017
MSMRemoveGroupDrift Removed attempted support for a mulit-token value for the --printcom=… Oct 26, 2016
PostFix *PostFIX edits to enable working with FIXMultiRun Jan 16, 2017
PostFreeSurfer *Add MSMSulc (currently untested) and some other minor changes Jan 16, 2017
PreFreeSurfer Changes for latest version of eddy used in Diffusion Preprocessing Oct 4, 2016
ReApplyFix Got all Matlab code to compile under Matlab R2013a on my workstation Jan 12, 2017
RestingStateStats Got all Matlab code to compile under Matlab R2013a on my workstation Jan 12, 2017
Supplemental/MakeAverageDataset Removed attempted support for a mulit-token value for the --printcom=… Oct 26, 2016
TaskfMRIAnalysis Modified some debugging outputs Feb 10, 2016
bedpostx Fixed bug in bedpostx README.md file Dec 21, 2016
fMRISurface Made all 7T 1res scripts executable Apr 27, 2016
fMRIVolume Fixed bug with use of ResultsFolder that I introduced in check in bef… Nov 14, 2016
global Got all Matlab code to compile under Matlab R2013a on my workstation Jan 12, 2017
.gitignore Make .gitignore ignore *.grad files to try to prevent proprietary fil… Aug 4, 2014
LICENSE.md Remove executable permission from text, configuration, and image files Apr 2, 2015
README.md Remove executable permission from text, configuration, and image files Apr 2, 2015
product.txt fixed uses of cp -p in FreeSurfer/scripts directory Mar 10, 2016
version.txt Added HCP's version of the bedpostx_gpu script Dec 21, 2016

README.md

HCP Pipelines

The HCP Pipelines product is a set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project. Among other things, these tools implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013

For further information, please see:

Discussion of HCP Pipeline usage and improvements can be posted to the hcp-users discussion list. Sign up for hcp-users at http://humanconnectome.org/contact/#subscribe