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What is your SUBJECTS_DIR set to? What do you get if you_______________________________________________
ls $SUBJECTS_DIR/ben
On 3/20/2020 9:48 AM, Peng Liu wrote:
External Email - Use Caution
Hi Andrew,
Thank you for your reply. I have tried this command you sent me
rm -rf $SUBJECTS_DIR/ben
It indeed deleted the ben folder under the subject directory, but when I try to run recon-all for this participant under another name, it still responds with the same error.
I have also tried the same data in another laptop. Also showed up the error. Would you say it might be something wrong with the data itself? (Although I am quite certain this is the raw T1 data which has never been performed any analysis).
Many Thanks
Peng--------------------------------------------
Peng Liu, PhD Candidate
Institut für Kognitive Neurologie und Demenzforschung (IKND)Otto-von-Guericke Universität MagdeburgDeutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland
Phone: +49 391 67 25074
On Fri, 20 Mar 2020 at 14:33, Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:
_______________________________________________Hi Peng,
Are you sure you’re deleting the subject folder from within the SUBJECTS_DIR?
rm -rf $SUBJECTS_DIR/ben
Should clear the issue.
best
Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Peng Liu <claudialiu1120@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, March 20, 2020 at 6:39 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).
External Email - Use Caution
Dear all,
I am trying to run recon-all command for a subject ben. Before I perform this command, I have exported SUBJECTS_DIR to a folder with only T1 data for this subject ben in it. However after I entered the command "recon-all -s ben -i T1.nii -all", this error showed up:
ERROR: You are trying to re-run an existing subject with (possibly)
new input data (-i). If this is truly new input data, you should delete
the subject folder and re-run, or specify a different subject name.
If you are just continuing an analysis of an existing subject, then
omit all -i flags.
I have tried all the suggestions listed in the error information, but none worked.
Does anyone have any suggestion? I would really appreciated it.
Many Thanks
Peng
--------------------------------------------
Peng Liu, PhD Candidate
Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland
Phone: +49 391 67 25074
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