On Fri, 20 Mar 2020 at 15:54, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

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 Magdeburg

Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217

39120 Magdeburg, Deutschland

Email: peng.liu@med.ovgu.de/Peng.Liu@dzne.de

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

Email: peng.liu@med.ovgu.de/Peng.Liu@dzne.de

Phone: +49 391 67 25074

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