Thank you, Doug.

Sorry for the misunderstanding but the folders for the individual subjects in my SUBJECTS_DIR already contain only the T1-MPRAGE-DICOMS and I only want to feed one DICOM per patient to the recon-all. My problem is the batch processing of several subjects using the following command:

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

the recon-all command requires me to specify one of the DICOM-files for each subject but each subject has different DICOM-file names. How can I specify that the command should just take any one DICOM-file within each subject folder? Using the wild card character * did not solve the problem.

Thanks!

/Ben

Am Di., 21. Jan. 2020 um 22:09 Uhr schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:

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
> 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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