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Update HippUnfold HCP processing #410

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0b7b658
Update HippUnfold HCP processing
orenpoliva Aug 25, 2026
9f9f02b
Address HippUnfold review comments
orenpoliva Aug 28, 2026
3b9ddb4
Update HippUnfold processing
orenpoliva Sep 8, 2026
3413238
Fix HippUnfold run scripts
orenpoliva Sep 8, 2026
02bf91c
Update HippUnfold processing
orenpoliva Sep 18, 2026
dcc4340
Update HippUnfold processing
orenpoliva Sep 18, 2026
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121 changes: 80 additions & 41 deletions Examples/Scripts/RunHippUnfoldHCP.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,14 @@
#!/bin/bash
#!/bin/bash

get_batch_options() {
local arguments=("$@")

command_line_specified_study_folder=""
command_line_specified_subject=""
command_line_specified_run_local="FALSE"
command_line_specified_run_local=""
command_line_specified_queue=""
command_line_specified_log_folder=""
command_line_specified_environment_script=""

local index=0
local numArgs=${#arguments[@]}
Expand All @@ -18,30 +21,59 @@ get_batch_options() {
--StudyFolder=*)
command_line_specified_study_folder=${argument#*=}
index=$(( index + 1 ))
;;
;;
--Subject=*)
command_line_specified_subject=${argument#*=}
index=$(( index + 1 ))
;;
;;
--runlocal)
command_line_specified_run_local="TRUE"
index=$(( index + 1 ))
;;
*)
echo ""
echo "ERROR: Unrecognized Option: ${argument}"
echo ""
exit 1
;;
;;
--QUEUE=*)
command_line_specified_queue=${argument#*=}
index=$((index + 1))
;;
--LogFolder=*)
command_line_specified_log_folder=${argument#*=}
index=$((index + 1))
;;
--EnvironmentScript=*)
command_line_specified_environment_script=${argument#*=}
index=$((index + 1))
;;
*)
echo ""
echo "ERROR: Unrecognized Option: ${argument}"
echo ""
exit 1
;;
esac
done
}

get_batch_options "$@"

###################################### DEFAULT PARAMETERS ######################################
# Edit these values as needed. Command-line options override the corresponding defaults.
StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by SubjectID)
Subjlist="100307 100610" #Space delimited list of subject IDs
EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script
EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script

# NOTE: syntax for QUEUE has changed compared to earlier pipeline releases,
# DO NOT include "-q " at the beginning
QUEUE=""
#QUEUE="hcp_priority.q"
################################################################################################

if [[ -n "$command_line_specified_environment_script" ]] ; then
EnvironmentScript="$command_line_specified_environment_script"
fi

if [[ ! -f "$EnvironmentScript" ]] ; then
echo "ERROR: Environment script does not exist: $EnvironmentScript" >&2
exit 1
fi

if [ -n "${command_line_specified_study_folder}" ]; then
StudyFolder="${command_line_specified_study_folder}"
Expand All @@ -51,44 +83,51 @@ if [ -n "${command_line_specified_subject}" ]; then
Subjlist="${command_line_specified_subject}"
fi

#Set up pipeline environment variables and software
if [[ "$command_line_specified_run_local" == "TRUE" ]] ; then
RunLocal="TRUE"
else
RunLocal="FALSE"
fi

# Set up pipeline environment variables and software
source "$EnvironmentScript"

# Log the originating call
echo "$@"

#NOTE: syntax for QUEUE has changed compared to earlier pipeline releases,
#DO NOT include "-q " at the beginning
#default to no queue, implying run local
QUEUE=""
#QUEUE="hcp_priority.q"

########################################## INPUTS ##########################################
LogFolder="$StudyFolder"
if [[ -n "$command_line_specified_log_folder" ]] ; then
LogFolder="$command_line_specified_log_folder"
fi
mkdir -p "$LogFolder"
cd "$LogFolder"

#Scripts called by this script do assume they run on the outputs of the PostFreeSurfer Pipeline
if [[ -n "$command_line_specified_queue" ]] ; then
QUEUE="$command_line_specified_queue"
fi

######################################### DO WORK ##########################################

for Subject in $Subjlist ; do
echo $Subject

if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then
echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh"
queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh)
else
echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh"
queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE")
fi

"${queuing_command[@]}" "$HCPPIPEDIR"/HippUnfoldHCP/HippUnfoldHCP.sh \
--study-folder="$StudyFolder" \
--subject="$Subject" \
# The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ...

echo "set -- --study-folder=$StudyFolder \
--subject=$Subject" \

echo ". ${EnvironmentScript}"
echo "$Subject"

if [[ "$RunLocal" == "TRUE" || -z "$QUEUE" ]] ; then
echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh"
queuing_command=("$HCPPIPEDIR/global/scripts/captureoutput.sh")

else

echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh"
queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE" -l "$LogFolder")

fi

"${queuing_command[@]}" \
Comment on lines +114 to +125

@coalsont coalsont Sep 19, 2026

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This is in a loop, it should be indented.

"$HCPPIPEDIR"/HippUnfoldHCP/HippUnfoldHCP.sh \
--study-folder="$StudyFolder" \
--subject="$Subject"

echo "set -- --study-folder=$StudyFolder --subject=$Subject"
echo ". ${EnvironmentScript}"

done
135 changes: 95 additions & 40 deletions Examples/Scripts/RunPostHippUnfoldHCP.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,15 @@
#!/bin/bash
#!/bin/bash

get_batch_options() {
local arguments=("$@")

command_line_specified_study_folder=""
command_line_specified_subject=""
command_line_specified_run_local="FALSE"
command_line_specified_run_local=""
command_line_specified_cortical_mesh=""
command_line_specified_queue=""
command_line_specified_log_folder=""
command_line_specified_environment_script=""

local index=0
local numArgs=${#arguments[@]}
Expand All @@ -18,30 +22,64 @@ get_batch_options() {
--StudyFolder=*)
command_line_specified_study_folder=${argument#*=}
index=$(( index + 1 ))
;;
;;
--Subject=*)
command_line_specified_subject=${argument#*=}
index=$(( index + 1 ))
;;
;;
--runlocal)
command_line_specified_run_local="TRUE"
index=$(( index + 1 ))
;;
*)
echo ""
echo "ERROR: Unrecognized Option: ${argument}"
echo ""
exit 1
;;
;;
--CorticalMesh=*)
command_line_specified_cortical_mesh=${argument#*=}
index=$(( index + 1 ))
;;
--LogFolder=*)
command_line_specified_log_folder=${argument#*=}
index=$(( index + 1 ))
;;
--QUEUE=*)
command_line_specified_queue=${argument#*=}
index=$(( index + 1 ))
;;
--EnvironmentScript=*)
command_line_specified_environment_script=${argument#*=}
index=$((index + 1))
;;
*)
echo ""
echo "ERROR: Unrecognized Option: ${argument}"
echo ""
exit 1
;;
esac
done
}

get_batch_options "$@"

###################################### DEFAULT PARAMETERS ######################################
# Edit these values as needed. Command-line options override the corresponding defaults.
StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by SubjectID)
Subjlist="100307 100610" #Space delimited list of subject IDs
EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script
CorticalMesh=32

# NOTE: syntax for QUEUE has changed compared to earlier pipeline releases,
# DO NOT include "-q " at the beginning
QUEUE=""
#QUEUE="hcp_priority.q"
################################################################################################

if [[ -n "$command_line_specified_environment_script" ]] ; then
EnvironmentScript="$command_line_specified_environment_script"
fi

if [[ ! -f "$EnvironmentScript" ]] ; then
echo "ERROR: Environment script does not exist: $EnvironmentScript" >&2
exit 1
fi

if [ -n "${command_line_specified_study_folder}" ]; then
StudyFolder="${command_line_specified_study_folder}"
Expand All @@ -51,44 +89,61 @@ if [ -n "${command_line_specified_subject}" ]; then
Subjlist="${command_line_specified_subject}"
fi

#Set up pipeline environment variables and software
if [[ "$command_line_specified_run_local" == "TRUE" ]] ; then
RunLocal="TRUE"
else
RunLocal="FALSE"
fi

# setting log folder
LogFolder="$StudyFolder"
if [[ -n "$command_line_specified_log_folder" ]] ; then
LogFolder="$command_line_specified_log_folder"
fi
mkdir -p "$LogFolder"
cd "$LogFolder"

# Set up pipeline environment variables and software
source "$EnvironmentScript"

# Log the originating call
echo "$@"

#NOTE: syntax for QUEUE has changed compared to earlier pipeline releases,
#DO NOT include "-q " at the beginning
#default to no queue, implying run local
QUEUE=""
#QUEUE="hcp_priority.q"

########################################## INPUTS ##########################################
if [[ -n "$command_line_specified_cortical_mesh" ]] ; then
CorticalMesh="$command_line_specified_cortical_mesh"
fi

#Scripts called by this script do assume they run on the outputs of the PostFreeSurfer Pipeline
if [[ -n "$command_line_specified_queue" ]] ; then
QUEUE="$command_line_specified_queue"
fi

######################################### DO WORK ##########################################
case "$CorticalMesh" in
32|59)
;;
*)
echo "ERROR: --CorticalMesh must be 32 or 59"
exit 1
;;
esac

for Subject in $Subjlist ; do
echo $Subject

if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then
echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh"
queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh)
else
echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh"
queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE")
fi

"${queuing_command[@]}" "$HCPPIPEDIR"/HippUnfoldHCP/PostHippUnfoldHCP.sh \
--study-folder="$StudyFolder" \
--subject="$Subject" \

# The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ...

echo "set -- --study-folder=$StudyFolder \
--subject=$Subject" \

echo ". ${EnvironmentScript}"
echo "$Subject"

if [[ "$RunLocal" == "TRUE" || -z "$QUEUE" ]] ; then
echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh"
queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh)
else
echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh"
queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE" -l "$LogFolder")
fi

"${queuing_command[@]}" "$HCPPIPEDIR"/HippUnfoldHCP/PostHippUnfoldHCP.sh --study-folder="$StudyFolder" --subject="$Subject" --cortical-mesh="$CorticalMesh"

# The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 $4...

echo "set -- --study-folder=$StudyFolder --subject=$Subject --cortical-mesh=$CorticalMesh"

echo ". ${EnvironmentScript}"

done
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