https://github.com/lennartverhagen/Pipelines
Revision 24e4f122404af3d3ca4686a28ffe19571482a9e4 authored by Matt Glasser on 11 December 2013, 22:41:44 UTC, committed by Matt Glasser on 11 December 2013, 22:41:44 UTC
1 parent e60eb03
Tip revision: 24e4f122404af3d3ca4686a28ffe19571482a9e4 authored by Matt Glasser on 11 December 2013, 22:41:44 UTC
*Modifications (renames, and additions) to global template files
*Modifications (renames, and additions) to global template files
Tip revision: 24e4f12
ReadMe.txt
The HCP Pipelines have the following software requirements:
*OS: 64bit Linux
*FSL 5.0.4 installed and config properly sourced
*FreeSurfer 5.2 installed and config properly sourced
*${HCPPIPEDIR}/src/gradient_unwarping installed with dependancies (source code located in this folder) if using gradient distortion correction
The HCP Pipelines reside in a root folder called ${HCPPIPEDIR}
${HCPPIPEDIR}/Examples/Scripts/SetUpHCPPipeline.sh will need to be edited to set the absolute path to this folder on your system.
This setup script must be sourced before running an HCP pipeline (examples below)
To test that the pipelines work, there is example data located in:
${HCPPIPEDIR}/Examples/792564
There are example batch scripts to call the pipelines on this data located in:
${HCPPIPEDIR}/Examples/Scripts
In all example batch scripts, the following variables will need to be modified prior to use:
StudyFolder="/media/myelin/brainmappers/Connectome_Project/TestStudyFolder" #Path to subject's data folder
${StudyFolder} needs to be changed to the location of the data that will be run.
Also EnvironmentScript="/media/2TBB/Connectome_Project/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script
Needs to be edited to reflect where this script is located on your system
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