for SubjectName in `cat *subs2.txt*`; do recon-all -i $SUBJECTS_DIR/$SubjectName/* -all -qcache; done

Output:

ERROR: Flag /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/Freesurfer_T1/SW1-1898_M12/EE018B6B unrecognized. -i /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/Freesurfer_T1/SW1-1898_M12/EE00C3C4 /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/Freesurfer_T1/SW1-1898_M12/EE018B6B ... (all remaining DICOM-files for the first subject)

How can I define one of my DICOM-files in the individual subject folders as input (the DICOM-file names are different for each subject)? I tried the character * (wild card) which did not work.

Many thanks for your support!

Best regards,

Benjamin