Hi,

Thanks for sending the exact commands and errors.

Your call syntax looks fine; this is a small bug in recon-all-clinical.sh in 8.1.0 that causes the then: then/endif not found message, rather than an issue with your arguments. 

It has been fixed in the dev branch by updating recon_all_clinical/recon-all-clinical.sh (see: https://github.com/freesurfer/freesurfer/blob/dev/recon_all_clinical/recon-all-clinical.sh)

You can either:

After that, you should be able to run:

recon-all-clinical.sh /full/path/to/T1.nii.gz SUBJECT_ID 6 /full/path/to/SUBJECTS_DI

Best,

Karthik

On Jan 5, 2026, at 12:36 PM, Sudhakar, Tejaswi <tejaswi.sudhakar@yale.edu> wrote:

        External Email - Use Caution        


Hi FreeSurfer Team,
 
I am trying to run the clinical pipeline using the 8.1.0 version. I was able to successfully run the pipeline using the 7.4 version using the approach (recon-all-clinical.sh /path/to/T1 [subject id] [threads] /path/to/SUBJECTS_DIR, without providing the input, subject, threads and sdir flags) but am getting the following errors when running it on the newest release. I have set the subjects directory as an environmental variable on attempted terminal test runs.
 
recon-all-clinical.sh ~T1//T1.nii.gz 1 6 ${SUBJECTS_DIR}
Unknown option: ~/T1/T1.nii.gz
Use -h or --help for usage information.
 
recon-all-clinical.sh ~T1/T1.nii.gz 1 6 ${SUBJECTS_DIR}
then: then/endif not found.
 
recon-all-clinical.sh -i ~/T1/T1.nii.gz -subjid 1 -threads 6 -sdir ~/fullcohort
then: then/endif not found.
 
recon-all-clinical.sh -i ~/T1/T1.nii.gz -subjid 1 -threads 6
 
SUBJECTS_DIR variable is empty.
Please provide a valid directory using the -sdir flag or set it as an environment variable.
 
Can you recommend any appropriate changes to my call to run the clinical pipeline? I can provide my full script if necessary.
 
_______________________________________________
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/