That means that you did not delete it. Delete it with the commands given
below and rerun
On 3/20/2020 11:23 AM, Peng Liu wrote:
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
<http://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
<mailto: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
<http://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 <mailto: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
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of
Peng Liu <claudialiu1...@gmail.com
<mailto:claudialiu1...@gmail.com>>
*Reply-To: *FS Help <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Date: *Friday, March 20, 2020 at 6:39 AM
*To: *FS Help <freesurfer@nmr.mgh.harvard.edu
<mailto: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
<http://peng....@med.ovgu.de/peng....@dzne.de>
Phone: +49 391 67 25074
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