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.