Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

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.liu@med.ovgu.de/Peng.Liu@dzne.de http://peng.liu@med.ovgu.de/Peng.Liu@dzne.de Phone: +49 391 67 25074

On Fri, 20 Mar 2020 at 15:54, Douglas N. Greve <dgreve@mgh.harvard.edu mailto: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
<http://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 <mailto: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
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of
    Peng Liu <claudialiu1120@gmail.com
    <mailto:claudialiu1120@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.liu@med.ovgu.de/Peng.Liu@dzne.de
    <http://peng.liu@med.ovgu.de/Peng.Liu@dzne.de>

    Phone: +49 391 67 25074

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