You can only specify one input dicom file. We have a tutorial on how to find that one file in a subject. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice
On 1/21/20 3:58 PM, Benjamin Ineichen wrote:
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Dear Freesurfer experts,
I try to run several subjects one after each other on recon-all using: 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
-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
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