Hi,

I'm using freesurfer to generate head surfaces using MRI file.

I want to execute recon-all command for number of subjects, but unable to run it.

The script I'm using is:

for i in `cat *subs.txt*`
do
    recon-all -s $i -all -qcache
done

subs.txt contains the name of folder that contains .nii file.

The scripts ends with the following error:

ERROR: no run data found in /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
have a volume called 001.mgz in  /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Please let me know how I can run recon-all for multiple subjects.

Thank you.

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