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
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.dehttp://peng.liu@med.ovgu.de/Peng.Liu@dzne.de Phone: +49 391 67 25074
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://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
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 Phone: +49 391 67 25074
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 CautionHi 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@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
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://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
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Hoopes, Andrew -
Peng Liu