Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
Is it having problems reading files (in the D state?). Matt. From: ARMAN PRAFUL KULKARNI mailto:apkulkar...@wisc.edu>> Date: Wednesday, October 10, 2018 at 3:55 PM To: Matt Glasser mailto:glass...@wustl.edu>>, Timothy Coalson mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh Hi Matt, Currently, this process is using 0.7% of the CPU--it doesn't appear to be the issue. In terms of where the pipeline is currently at, from the output script (PostFreeSurferPipeline.sh.o) it has been stuck on the following for the past hour or greater: parsed 'var * -1' as '(var*(-1))' parsed 'var * -1' as '(var*(-1))' parsed 'var * -1' as '(var*(-1))' parsed 'abs(thickness)' as 'abs(thickness)' parsed 'thickness > 0' as '(thickness>0)' parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))' parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))' parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))' parsed '(atlas + individual) > 0' as '((atlas+individual)>0)' parsed 'var * -1' as '(var*(-1))' parsed 'var * -1' as '(var*(-1))' parsed 'var * -1' as '(var*(-1))' parsed 'abs(thickness)' as 'abs(thickness)' parsed 'thickness > 0' as '(thickness>0)' parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))' parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))' parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))' parsed '(atlas + individual) > 0' as '((atlas+individual)>0)' Also, for the error output file (PostFreeSurferPipeline.sh.e), this seems to be the most recent output: WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Sincerely, Arman From: Glasser, Matthew mailto:glass...@wustl.edu>> Sent: Wednesday, October 10, 2018 3:28:28 PM To: ARMAN PRAFUL KULKARNI; NEUROSCIENCE tim Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh What is using the CPU? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of ARMAN PRAFUL KULKARNI mailto:apkulkar...@wisc.edu>> Date: Wednesday, October 10, 2018 at 3:27 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh Hi Tim, I have the updated version of workbench now, and have tried running the pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5 hours. To my knowledge, prior to this update, it only took around 45 minutes when successful. Is this normal for this version of the pipeline to take this long? Thanks again. Sincerely, Arman From: Timothy Coalson mailto:tsc...@mst.edu>> Sent: Tuesday, October 9, 2018 6:13:44 PM To: ARMAN PRAFUL KULKARNI Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh You need to update workbench to the latest release, that option is a recent addition to the command that is failing. Tim On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI mailto:apkulkar...@wisc.edu>> wrote: Hi, I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh file. I have been able to run PreFreeSurferPipelineBatch.sh and FreeSurferPipelineBatch.sh with no issues. However, when running PostFreeSurferPipelineBatch.sh, I get the following error after around 10 minutes of the script running: "ERROR: Unexpected parameter: -local-affine-method", and I am not sure how to proceed. I appreciate any insight into this problem. Sincerely, Arman --- #!/bin/bash echo "This script must be SOURCED to correctly setup the environment prior to running any of the othe
Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
Hi Matt,
Currently, this process is using 0.7% of the CPU--it doesn't appear to be the
issue. In terms of where the pipeline is currently at, from the output script
(PostFreeSurferPipeline.sh.o) it has been stuck on the following for the past
hour or greater:
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'abs(thickness)' as 'abs(thickness)'
parsed 'thickness > 0' as '(thickness>0)'
parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed '(atlas + individual) > 0' as '((atlas+individual)>0)'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'abs(thickness)' as 'abs(thickness)'
parsed 'thickness > 0' as '(thickness>0)'
parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed '(atlas + individual) > 0' as '((atlas+individual)>0)'
Also, for the error output file (PostFreeSurferPipeline.sh.e), this seems to be
the most recent output:
WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to
'WM-RH-UNKNOWN_1'
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 76 entries read (originally
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 76 entries read (originally
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
Sincerely,
Arman
From: Glasser, Matthew
Sent: Wednesday, October 10, 2018 3:28:28 PM
To: ARMAN PRAFUL KULKARNI; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
What is using the CPU?
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of ARMAN PRAFUL KULKARNI
mailto:apkulkar...@wisc.edu>>
Date: Wednesday, October 10, 2018 at 3:27 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
Hi Tim,
I have the updated version of workbench now, and have tried running the
pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5
hours. To my knowledge, prior to this update, it only took around 45 minutes
when successful. Is this normal for this version of the pipeline to take this
long? Thanks again.
Sincerely,
Arman
From: Timothy Coalson mailto:tsc...@mst.edu>>
Sent: Tuesday, October 9, 2018 6:13:44 PM
To: ARMAN PRAFUL KULKARNI
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.
Tim
On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI
mailto:apkulkar...@wisc.edu>> wrote:
Hi,
I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh
file. I have been able to run PreFreeSurferPipelineBatch.sh and
FreeSurferPipelineBatch.sh with no issues. However, when running
PostFreeSurferPipelineBatch.sh, I get the following error after around 10
minutes of the script running: "ERROR: Unexpected parameter:
-local-affine-method", and I am not sure how to proceed. I appreciate any
insight into this problem.
Sincerely,
Arman
---
#!/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 #) a
Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
What is using the CPU?
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of ARMAN PRAFUL KULKARNI
mailto:apkulkar...@wisc.edu>>
Date: Wednesday, October 10, 2018 at 3:27 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
Hi Tim,
I have the updated version of workbench now, and have tried running the
pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5
hours. To my knowledge, prior to this update, it only took around 45 minutes
when successful. Is this normal for this version of the pipeline to take this
long? Thanks again.
Sincerely,
Arman
From: Timothy Coalson mailto:tsc...@mst.edu>>
Sent: Tuesday, October 9, 2018 6:13:44 PM
To: ARMAN PRAFUL KULKARNI
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.
Tim
On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI
mailto:apkulkar...@wisc.edu>> wrote:
Hi,
I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh
file. I have been able to run PreFreeSurferPipelineBatch.sh and
FreeSurferPipelineBatch.sh with no issues. However, when running
PostFreeSurferPipelineBatch.sh, I get the following error after around 10
minutes of the script running: "ERROR: Unexpected parameter:
-local-affine-method", and I am not sure how to proceed. I appreciate any
insight into this problem.
Sincerely,
Arman
---
#!/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
#source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}//HCP/Pipelines
#export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export CARET7DIR=/usr/local/workbench/bin_linux64
export HCPPIPEDIR_Templates=${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 MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll
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Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
Hi Tim,
I have the updated version of workbench now, and have tried running the
pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5
hours. To my knowledge, prior to this update, it only took around 45 minutes
when successful. Is this normal for this version of the pipeline to take this
long? Thanks again.
Sincerely,
Arman
From: Timothy Coalson
Sent: Tuesday, October 9, 2018 6:13:44 PM
To: ARMAN PRAFUL KULKARNI
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.
Tim
On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI
mailto:apkulkar...@wisc.edu>> wrote:
Hi,
I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh
file. I have been able to run PreFreeSurferPipelineBatch.sh and
FreeSurferPipelineBatch.sh with no issues. However, when running
PostFreeSurferPipelineBatch.sh, I get the following error after around 10
minutes of the script running: "ERROR: Unexpected parameter:
-local-affine-method", and I am not sure how to proceed. I appreciate any
insight into this problem.
Sincerely,
Arman
---
#!/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
#source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}//HCP/Pipelines
#export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export CARET7DIR=/usr/local/workbench/bin_linux64
export HCPPIPEDIR_Templates=${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 MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll
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Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.
Tim
On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI
wrote:
> Hi,
>
> I have been running the HCP Pipeline (v 3.27.0) on one subject's
> unprocessed data from the HCP-1200 dataset. Below is what I have in the
> SetUpHCPPipeline.sh file. I have been able to run
> PreFreeSurferPipelineBatch.sh and FreeSurferPipelineBatch.sh with no
> issues. However, when running PostFreeSurferPipelineBatch.sh, I get the
> following error after around 10 minutes of the script running: "ERROR:
> Unexpected parameter: -local-affine-method", and I am not sure how to
> proceed. I appreciate any insight into this problem.
>
> Sincerely,
> Arman
> ---
>
> #!/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
> #source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
>
> # Set up specific environment variables for the HCP Pipeline
> export HCPPIPEDIR=${HOME}//HCP/Pipelines
> #export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
> export CARET7DIR=/usr/local/workbench/bin_linux64
>
> export HCPPIPEDIR_Templates=${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 MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll
>
> ___
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>
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[HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh
Hi,
I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh
file. I have been able to run PreFreeSurferPipelineBatch.sh and
FreeSurferPipelineBatch.sh with no issues. However, when running
PostFreeSurferPipelineBatch.sh, I get the following error after around 10
minutes of the script running: "ERROR: Unexpected parameter:
-local-affine-method", and I am not sure how to proceed. I appreciate any
insight into this problem.
Sincerely,
Arman
---
#!/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
#source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}//HCP/Pipelines
#export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export CARET7DIR=/usr/local/workbench/bin_linux64
export HCPPIPEDIR_Templates=${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 MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll
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