Each subject needs to be processed separately. You can loop through your subjects, and submit recon-all for each one.

From: Huaiyu Liu <huaiyu.liu@ucl.ac.uk>
Sent: Tuesday, June 9, 2026 10:36 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Recon-all for multiple subjects on parallel

        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