Re: [Freesurfer] Help with script with 7.2 on an HPC

[Huang, Yujing]

Hi Lisa,

You can find information about those scripts here 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

Executing the corresponding script with the flag -help should provide some 
information too.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Taylor, Lisa
Sent: Monday, February 6, 2023 6:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Help with script with 7.2 on an HPC


        External Email - Use Caution
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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