External Email - Use Caution        

Not a developer, but this is something that comes up frequently in most analysis situations.

For qsub, you should be able to just make separate scripts for each subject and submit them all at once and let the scheduler node handle the rest. 

E.g. If you have sub1.sh, sub2.sh,....subn.sh as the submission scripts you can just submit them all:

for j in sub*.sh; do
qsub ${j}
done

You may consider writing a wrapper that will create all the subscripts based on an input...e.g.:


SUBNAME=$1

Echo "#!/bin/bash
#$ -cwd
#$ -o /data/holly-host/UserName/logs/
#$ -j y
#$ -S /bin/bash
#$ -N reconall

export FREESURFER_HOME=/usr/local/freesurfer/8.2.0-1
export FS_LICENSE=/usr/local/freesurfer/8.2.0-1/license.txt
export SUBJECTS_DIR=/data/holly-host/hliu/freesurfer_subjects

source $FREESURFER_HOME/SetUpFreeSurfer.sh

mkdir -p $SUBJECTS_DIR

env | grep -E "FREESURFER|FS_LICENSE|SUBJECTS_DIR"

recon-all -all -i /data/holly-host/UserName/anat/${SUBNAME}_t1w.nii -s sub-01
SegmentAAN.sh sub-01

" > ${SUBNAME}.sh




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Subject: [EXTERNAL] Freesurfer Digest, Vol 268, Issue 8
 
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   1. Re: Recon-all for multiple subjects on parallel (Huaiyu Liu)


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Message: 1
Date: Tue, 9 Jun 2026 14:35:49 +0000
From: Huaiyu Liu <huaiyu.liu@ucl.ac.uk>
Subject: [Freesurfer] Re: Recon-all for multiple subjects on parallel
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <DB8PR01MB5899E8997D209D3F51B01799DB1D2@DB8PR01MB5899.eurp
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        External Email - Use Caution

Dear FS Developers,

I recently asked a question about how to run recon-all in parallel for multiple subjects (like 4-8).
Could someone give me some clues, I would be really apperciate.

Best,
Huaiyu
________________________________
From: Huaiyu Liu <huaiyu.liu@ucl.ac.uk>
Sent: Thursday, May 28, 2026 18:21
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Recon-all for multiple subjects on parallel

Dear FreeSurfer Developers,

I am using the following code on my department's HPC to (1) reconstruct a single participant’s T1w image and (2) perform brainstem segmentation.
The code works well, but I have 40 participants in total. Hence, I wonder how I can run recon-all and brainstem segmentation for multiple subjects in parallel.
Could you tell me the code?

1) FreeSurfer version: --freesurfer-linux 8.2.0-1 on my department's HPC (high-performance cluster)

2) My shell script for recon-all and brainstem segmentation for single subject:
#!/bin/bash
#$ -cwd
#$ -o /data/holly-host/UserName/logs/
#$ -j y
#$ -S /bin/bash
#$ -N reconall

export FREESURFER_HOME=/usr/local/freesurfer/8.2.0-1
export FS_LICENSE=/usr/local/freesurfer/8.2.0-1/license.txt
export SUBJECTS_DIR=/data/holly-host/hliu/freesurfer_subjects

source $FREESURFER_HOME/SetUpFreeSurfer.sh

mkdir -p $SUBJECTS_DIR

env | grep -E "FREESURFER|FS_LICENSE|SUBJECTS_DIR"

recon-all -all -i /data/holly-host/UserName/anat/sub-01_t1w.nii -s sub-01
SegmentAAN.sh sub-01

3) My command for submit the jobs to the cluster with 32 GB of RAM request

qsub -l vf=32G -l h_vmem=32G reconall

Thank you very much for your time and consideration, I look forward to hearing from you.

Best,
Huaiyu
_________________________________________
Huaiyu Liu (Ted)
Postdoctoral Research Fellow
Department of Imaging Neuroscience, Functional Imaging Laboratory
University College London
12 Queen Square, London WC1N 3AR






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