When you run
recon-all -s HPTU_vol11_2012 -i pacsfiles/MPRAGE.Ser1.Img0.dcm
Does the folder or file called $SUBJECTS_DIR/HPTU_vol11_2012 already exist?
doug
On 09/14/2012 05:00 PM, Carolina Valencia wrote:
> first rename folder *dicom* to *pacsfiles*
> then run
> cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/HPTU_vol11_2012$
>
> recon-all -s HPTU_vol11_2012 -i pacsfiles/MPRAGE.Ser1.Img0.dcm
> then with a bulk rename files program rename *MPRAGE*.Ser1.Img0.dcm
> ... to *T13D*.Ser1.Img0.dcm...
> then run
> cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/HPTU_vol11_2012$
>
> recon-all -s HPTU_vol11_2012 -i pacsfiles/T13D.Ser1.Img0.dcm
>
> I usually use tab in order to doesn't make mistakes and typos.
>
> Thanks,
>
>
> 2012/9/14 Douglas N Greve <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
>
> what did you rename it to and what is your command line after you
> rename it?
>
>
> On 09/14/2012 04:48 PM, Carolina Valencia wrote:
>
> As I said in the first email I tried the suggestions in the
> message, rename the files, folders, eliminate the folders,
> starts from scratch etc and again with your answer, I rename
> the folder of dicom, and rename the MPRAGE files and anything
> works, still the same message.
> Thank you,
>
>
> 2012/9/14 Douglas N Greve <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>
>
>
> The error output below tells you what to do. If the
> subject folder
> (HPTU_vol11_2012) already exists. Since it has your dicom
> data in
> it, you should not delete it. Instead, rename that
> directory and
> keep your command-line (changing the -i path to point to
> the new
> dicom file but keeping the same subject name), or change
> the name
> of the subject.
> doug
>
>
>
>
> On 09/14/2012 03:44 PM, Carolina Valencia wrote:
>
> the directory exists and trying without / doesn't
> change anything,
> any advice?
> One week ago, I was processing with the same command
> line with
> other subjects without problems,
>
> 2012/9/14 Douglas N Greve <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>>
>
>
> And before you run this, does
> $SUBJECTS_DIR/HPTU_vol11_2012 exist?
> BTW, try it without a slash at the end of the name.
> doug
>
>
> On 09/14/2012 02:09 PM, Carolina Valencia wrote:
>
>
> Sure!
>
>
> cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria$
> recon-all -s HPTU_vol11_2012/ -i
> HPTU_vol11_2012/dicom/MPRAGE.Ser1.Img0.dcm
>
> 2012/9/14 Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>>>
>
>
> What is your command line?
> doug
>
>
>
> On 09/14/2012 12:23 PM, Carolina Valencia
> wrote:
> > Hi Freesurfer users:
> >
> > I'm trying to run recon-all command in a single subject and
> > I don't know why always there is an error message about the
> names, I
> > tried the suggestionsin the message, rename the files, folders,
> > eliminate the folders etc
> > But I don't succeed to star to running my data.
> > Many thanks,
> >
> >
> > 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.
> >
> > --
> > --
> > *Carolina Valencia Muñoz*
> >
> >
> >
> >
> > _______________________________________________
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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> -- --
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
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>
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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