ERROR: 'recon-all' command failed with return code: 1

[Austin Cooper]

Hi there.

Can anyone suggest the reason behind this error, when running freesurferPipelineBatch.sh? I can't seem to find a problem with the code.

Could it be because i already ran this subject with the script and it didn't finish and now I''m restarting the whole script from scratch on the data that was already partially analysed? Or is it that no input image is being found by recon-all?

Any assistance would be greatly appreciated!

 ./FreeSurferPipelineBatch.sh

023
About to use fsl_sub to queue or run /data/shmuel/shmuel1/austin/HCPpipelines-master/FreeSurfer/FreeSurferPipeline.sh
Error submitting job - Tue May 31 17:20:45 EDT 2022:FreeSurferPipeline-v5.3.0-HCP.sh: While running '/data/shmuel/shmuel1/austin/HCPpipelines-master/FreeSurfer/FreeSurferPipeline-v5.3.0-HCP.sh --subject=023 --subjectDIR=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w --t1=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w/T2w_acpc_dc_restore.nii.gz':
Tue May 31 17:20:45 EDT 2022:FreeSurferPipeline-v5.3.0-HCP.sh: ERROR: 'recon-all' command failed with return code: 1

set -- --subject=023       --subjectDIR=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w       --t1=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w/T1w_acpc_dc_restore.nii.gz       --t1brain=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w/T1w_acpc_dc_restore_brain.nii.gz       --t2=/data/shmuel/shmuel1/austin/MGH-subjects/rsfmri/023/T1w/T2w_acpc_dc_restore.nii.gz
. /data/shmuel/shmuel1/austin/HCPpipelines-master/Examples/Scripts/SetUpHCPPipeline.sh

[Glasser, Matt]

It is the existing subject issue. 

 

Matt.

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