External Email - Use Caution Hello Douglas,
If I do ls $SUBJECTS_DIR/ben, the T1 image will show up as predicted. However if I tried to recon-all, the error will pop up. Many Thanks -------------------------------------------- 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....@med.ovgu.de/peng....@dzne.de Phone: +49 391 67 25074 On Fri, 20 Mar 2020 at 15:54, Douglas N. Greve <dgr...@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....@med.ovgu.de/peng....@dzne.de > Phone: +49 391 67 25074 > > > On Fri, 20 Mar 2020 at 14:33, Hoopes, Andrew <ahoo...@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-boun...@nmr.mgh.harvard.edu> on behalf of Peng Liu < >> claudialiu1...@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....@med.ovgu.de/peng....@dzne.de >> >> Phone: +49 391 67 25074 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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
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