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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 CautionDear 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
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
freesurfer@nmr.mgh.harvard.edu
-
Benjamin Ineichen -
Greve, Douglas N.,Ph.D.