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Hi there,
I am trying to update my scripts on our university's HPC but am running into an
issue. I am not too savvy when it comes to this, so I apologize. My guess is I
will have to run my old 6.0 script but without the -hippocampal-subfields-T1
argument in the new 7.2 script that I copied over, but then run the
'segmentHA_T1.sh' separately? Is there a way to incorporate this script in the
7.2 script I currently have? Thank you for any help/insight you can give.
Error I get when trying to run my updated 7.2 script:
$cat slurm-19565158.out
ERROR: the hippocampal subfield module is now in separate scripts:
segmentHA_T1.sh
segmentHA_T2.sh
segmentHA_T1_long.sh
1 of 2 of the scripts used to run freesurfer on the HPC3:
cat freesurfer_template_7.2.sub
#!/bin/bash
#SBATCH --job-name=fs_reconall_subid
#SBATCH -A account
#SBATCH -p user
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --error=slurm-reconall_subid.err
#SBATCH --mem-per-cpu=18gb
module load freesurfer/7.2.0
xport SUBJECTS_DIR=imagedir
source $FREESURFER_HOME/SetUpFreeSurfer.sh
# run freesurfer
srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all
-hippocampal-subfields-T1 -brainstem-structures -qcache
2 of 2 of the script used to run freesurfer on the HPC3:
cat 7.2_freesurfer_prep_single_subj.sh
#!/bin/sh
# usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge]
[freesurfer_subj_folder]
# [queue] = free | standard
# [account_to_charge] = ltaylor2
# [freesurfer_subj_folder] = This is the subject directory created by
freesurfer for processing
#
if [[ $# -lt 3 ]] ; then
echo 'Usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge]
[freesurfer_subj_folder]'
echo '[queue] = free | standard'
echo '[account_to_charge] = ltaylor2'
echo 'PLEASE ONLY USE THE FREE QUEUE UNLESS OTHERWISE INSTRUCTED'a
echo '[freesurfer_subj_folder] = This is the subject directory created by
freesurfer for processing'
exit 0
fi
subids=$3
imagedir=`echo $PWD`
echo $subids
if [ -d freesurfer_sub ]; then
echo directory freesurfer_sub exists ...;
else
mkdir freesurfer_sub;
fi
for subid in ${subids}; do
sed -e s/subid/${subid}/g -e s/user/${1}/g -e s/account/${2}/g -e
s#imagedir#${imagedir}#g freesurfer_template_7.2.sub >
freesurfer_sub/fs_${subid}.sub
cd freesurfer_sub
echo sbatch fs_${subid}.sub
sbatch fs_${subid}.sub
cd ..
done
Thank you!
Lisa
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