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fMRISurface related pull request #136

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merged 9 commits into from
Oct 12, 2019
Merged

fMRISurface related pull request #136

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72d1510
fMRISurface pipeline related changes
sivcek Sep 27, 2019
462b4d5
Switched to using mppmodecheck.shlib.
sivcek Sep 29, 2019
bc5b62a
Adjusted compliance check.
sivcek Oct 2, 2019
02d3ee9
Removed compliance check as it is not needed.
sivcek Oct 3, 2019
9ef5726
Removed sourcing the mppmodecheck.shlib.
sivcek Oct 3, 2019
27719cf
Set MSMSulc as the default registration option and added warning when…
sivcek Oct 9, 2019
d7c9334
Fixed a log_Warn bug, changed wording.
sivcek Oct 9, 2019
c447c16
Corrected a typo in warn message.
sivcek Oct 9, 2019
c160585
Split the warning into multiple lines.
sivcek Oct 10, 2019
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20 changes: 12 additions & 8 deletions fMRISurface/GenericfMRISurfaceProcessingPipeline.sh
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Original file line number Diff line number Diff line change
@@ -1,24 +1,24 @@
#!/bin/bash
#!/bin/bash
set -e

# Requirements for this script
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP) , gradunwarp (HCP version 1.0.2)
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP) , gradunwarp (HCP version 1.0.2)
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# environment: use SetUpHCPPipeline.sh (or individually set FSLDIR, FREESURFER_HOME, HCPPIPEDIR, PATH - for gradient_unwarp.py)

########################################## PIPELINE OVERVIEW ##########################################
########################################## PIPELINE OVERVIEW ##########################################

# TODO

########################################## OUTPUT DIRECTORIES ##########################################
########################################## OUTPUT DIRECTORIES ##########################################

# TODO

# --------------------------------------------------------------------------------
# Load Function Libraries
# --------------------------------------------------------------------------------

source $HCPPIPEDIR/global/scripts/log.shlib # Logging related functions
source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
source ${HCPPIPEDIR}/global/scripts/log.shlib # Logging related functions
source ${HCPPIPEDIR}/global/scripts/opts.shlib # Command line option functions

################################################ SUPPORT FUNCTIONS ##################################################

Expand Down Expand Up @@ -56,8 +56,8 @@ SmoothingFWHM=`opts_GetOpt1 "--smoothingFWHM" $@` # "${14}"
GrayordinatesResolution=`opts_GetOpt1 "--grayordinatesres" $@` # "${14}"
RegName=`opts_GetOpt1 "--regname" $@`

if [ "${RegName}" = "" ]; then
RegName="FS"
if [ -z "${RegName}" ]; then
RegName="MSMSulc"
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fi

RUN=`opts_GetOpt1 "--printcom" $@` # use ="echo" for just printing everything and not running the commands (default is to run)
Expand All @@ -72,6 +72,10 @@ log_Msg "GrayordinatesResolution: ${GrayordinatesResolution}"
log_Msg "RegName: ${RegName}"
log_Msg "RUN: ${RUN}"

if [ "${RegName}" = "FS" ] ; then
log_Warn "WARNING: FreeSurfer's surface registration (based on cortical folding) is deprecated in the HCP Pipelines as it results in poorer cross-subject functional and cortical areal alignment relative to MSMSulc. Additionally, FreeSurfer registration results in dramatically higher surface distortion (both isotropic and anisotropic). These things occur because FreeSurfer's registration has too little regularization of folding patterns that are imperfectly correlated with function and cortical areas, resulting in overfitting of folding patterns. See Robinson et al 2014, 2018 Neuroimage, and Coalson et al 2018 PNAS for more details."
fi

# Setup PATHS
PipelineScripts=${HCPPIPEDIR_fMRISurf}

Expand Down
21 changes: 13 additions & 8 deletions fMRISurface/GenericfMRISurfaceProcessingPipeline_1res.sh
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Original file line number Diff line number Diff line change
@@ -1,24 +1,24 @@
#!/bin/bash
#!/bin/bash
set -e

# Requirements for this script
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP) , gradunwarp (HCP version 1.0.2)
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP) , gradunwarp (HCP version 1.0.2)
# environment: use SetUpHCPPipeline.sh (or individually set FSLDIR, FREESURFER_HOME, HCPPIPEDIR, PATH - for gradient_unwarp.py)

########################################## PIPELINE OVERVIEW ##########################################
########################################## PIPELINE OVERVIEW ##########################################

# TODO

########################################## OUTPUT DIRECTORIES ##########################################
########################################## OUTPUT DIRECTORIES ##########################################

# TODO

# --------------------------------------------------------------------------------
# Load Function Libraries
# --------------------------------------------------------------------------------

source $HCPPIPEDIR/global/scripts/log.shlib # Logging related functions
source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
source ${HCPPIPEDIR}/global/scripts/log.shlib # Logging related functions
source ${HCPPIPEDIR}/global/scripts/opts.shlib # Command line option functions

################################################ SUPPORT FUNCTIONS ##################################################

Expand Down Expand Up @@ -56,8 +56,8 @@ SmoothingFWHM=`opts_GetOpt1 "--smoothingFWHM" $@` # "${14}"
GrayordinatesResolution=`opts_GetOpt1 "--grayordinatesres" $@` # "${14}"
RegName=`opts_GetOpt1 "--regname" $@`

if [ "${RegName}" = "" ]; then
RegName="FS"
if [ -z "${RegName}" ]; then
RegName="MSMSulc"
fi

RUN=`opts_GetOpt1 "--printcom" $@` # use ="echo" for just printing everything and not running the commands (default is to run)
Expand All @@ -72,6 +72,11 @@ log_Msg "GrayordinatesResolution: ${GrayordinatesResolution}"
log_Msg "RegName: ${RegName}"
log_Msg "RUN: ${RUN}"

if [ "${RegName}" = "FS" ] ; then
logWarn "WARNING: FreeSurfer registration is deprecated in the HCP Pipelines as it results in poorer cross-subject functional and cortical areal alignment relative to MSMSulc. Additionally, FreeSurfer registration results in dramatically higher surface distortion (both isotropic and anisotropic). These things occur because FreeSurfer's registration has too little regularizattion of folding patterns that are imperfectly correlated with function and cortical areas, resulting in overfitting of folding patterns. See Robinson et al 2014, 2018 Neuroimage, and Coalson et al 2018 PNAS for more details."
fi


# Setup PATHS
PipelineScripts=${HCPPIPEDIR_fMRISurf}

Expand Down