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: > > External Email - Use Caution > > 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 > ineic...@protonmail.ch <mailto:ineic...@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 > ineic...@protonmail.ch <mailto:ineic...@protonmail.ch> > +41 76 391 04 01 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
