Hi Michael,
Thank you for sharing the results of your debugging efforts.
In response to your message and to some difficulties/questions that
students had in the recent HCP course, I have changed the example
SetUpHCPPipeline.sh script in the Examples/Scripts directory so that it
looks like the code below (my additions are in red.) I believe these
changes should ensure that FreeSurfer as used in the Pipelines will use
the same version of FSL as the pipelines themselves are using.
These changes have been checked in to the repository, but are not yet
included in a released version of the scripts. They will be included in
the next release.
Please feel free to let me know if you see any further error in
the logic.
Thanks,
Tim
#!/bin/bash
echo "This script must be SOURCED to correctly setup the environment
prior to running any of the other HCP scripts contained here"
# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the
# FSLDIR setting for your setup
#export FSLDIR=/usr/share/fsl/5.0
#. ${FSLDIR}/etc/fslconf/fsl.sh
# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses FSL_DIR instead of FSLDIR to determine the FSL version
export FSL_DIR="${FSLDIR}"
# Set up FreeSurfer (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the
# FREESURFER_HOME setting for your setup
#export FREESURFER_HOME=/usr/local/bin/freesurfer
#. ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}/projects/Pipelines
export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config
export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export MSMBin=${HCPPIPEDIR}/MSMBinaries
On Wed, Jun 17, 2015, at 14:49, m s wrote:
> Version 3.4.0
>
> Hi again,
>
> We've come across a problem that others may want to know about.
>
> The FSL setup scripts defines FSLDIR itself. FSL_DIR must be defined
> for freesurfer, to know what fsl version to use. The freesurfer setup
> script SetUpFreeSurfer.sh calls FreeSurferEnv.sh, which only sets
> FSL_DIR if it's not already set. So if freesurfer is setup in a user's
> .bash_profile (or similar), running SetUpFreeSurfer.sh from an HCP
> pipelines setup script will NOT change FSL_DIR if you're already
> pointing to a diff version of FSL than your .bash_profile.
>
> -M
>
> _______________________________________________
>
HCP-Users mailing list
>
[email protected]
>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
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