Hi Antonin and Tim
you should be able to do:
setenv FS_SKIP_TAGS 1
mri_convert vol_with_tags.mgz vol_without_tags.mgz
and verify it worked with mri_info
cheers
Bruce
On Tue, 21 Jan 2020, Antonin Skoch wrote:
External Email - Use Caution
Hi, Tim,
the subject ID can be also contained in the commandline history which is sto
red in .mgz files. This can be viewed using
mri_info file.mgz --cmds
I am not aware of any direct command which can strip out this info, but you
surely could convert .mgz file to .nii and then (using path which does not c
ontain subject ID) convert back to .mgz, if needed.
Antonin
Hi Doug,
thanks for the mri_add_xform_to_header idea, I didn't know about that option
!
Best,
Tim
> On January 21, 2020 at 4:24 PM "Greve, Douglas N.,Ph.D."
> <dgr...@mgh.harvard.edu> wrote:
>
>
>
> For the mgz volumes, you should be able to do something like
> mri_add_xform_to_header -c /new/path/to/xfm brain.mgz
>
> For the labels you could just use something like
> sed s/oldsubjectname/newsubjectname
>
>
>
>
> On 1/17/2020 3:48 AM, Tim Schäfer wrote:
> > External Email - Use Caution
> >
> > Hi Douglas,
> >
> > sure, you can get two example files here:
> >
> > wget http://rcmd.org/tmp/brain.mgz
> > wget http://rcmd.org/tmp/lh.BA1_exvivo.label
> >
> > The brain volume contains the ID because it stores the full path to the
> > tairach xfm (which includes the folder name, so the ID). You can check b
y:
> >
> > mri_info brain.mgz | grep talair
> >
> > (In this case the ID is 'tim').
> >
> > Without mri_info, you can get it as well:
> >
> > mv brain.mgz brain.gz
> > gunzip -c brain.gz | strings | grep talair
> >
> > The second file is an ASCII label from the same subject. You can get the
ID
> > by running:
> >
> > head -n 1 lh.BA1_exvivo.label
> >
> > There are some other files which contain the ID, these are just 2 exampl
es.
> >
> >
> > I am currently in contact with the people running the consortium server
and
> > I am not really sure whether the rule that the ID must not be in the fil
es
> > makes any sense at all. Maybe I can get around this.
> >
> >
> > Best,
> >
> > Tim
> >
> >
> >
> >
> >> On January 17, 2020 at 12:23 AM "Greve, Douglas N.,Ph.D."
> >> <dgr...@mgh.harvard.edu> wrote:
> >>
> >>
> >> Hi Tim, can you send a list of files that have the identifier. For
> >> volumes and surfaces, it might be as easy as running
> >> mri_convert/mris_convert using the same file as input and output.
> >>
> >> On 1/13/2020 5:54 AM, Tim Schäfer wrote:
> >>> External Email - Use Caution
> >>>
> >>> Dear FreeSurfer experts,
> >>>
> >>>
> >>> I have two questions on subject IDs in FreeSurfer output.
> >>>
> >>> 1) is it possible to change to subject identifier in the FreeSurfer
> >>> output after recon-all has been run?
> >>>
> >>> Background: I would like to upload data pre-processed with FreeSurfer
to
> >>> a consortium server. The subject ID is a random identifier, but the
> >>> upload guidelines say this identifier must only occur in certain file
> >>> types (Excel files, .log files, and some more, but not in any other
> >>> files).
> >>>
> >>> I noticed that a lot of the output files produced by FreeSurfer contai
n
> >>> the subject identifier somewhere, including various binary files, so I
> >>> guess there is no easy way to change it. But maybe there is? Like
> >>> rerunning a part of recon-all?
> >>>
> >>>
> >>>
> >>> 2) If not, I could rename the source NIFTI files (e.g., from the
> >>> identifiers to something like 'subject001', 'subject002', ...) and
> >>> re-process everything. This would take some computational time for the
>
> >>> 500 subjects, but it would be okay I guess.
> >>>
> >>> But a large number of the subjects have manual edits applied already.
Is
> >>> there a way to keep the manual edits? E.g., I thought maybe I could
> >>> rename the individual directories of the edited subjects, leave the
> >>> edited files in there, and run recon-all again. But what would happen?
> >>> Will the new output files have the renamed ID from the directory name
> >>> (and thus the recon-all command line), or will they still use the old
ID
> >>> (from the header of the existing files)? Or will the existing, edited
> >>> files which contain a different ID be ignored during the new run becau
se
> >>> the IDs do not match, and thus the existing edits would have no effect
?
> >>>
> >>>
> >>> All the best,
> >>>
> >>> Tim
> >>>
> >>> --
> >>> Dr. Tim Schäfer
> >>> Postdoc Computational Neuroimaging
> >>> Department of Child and Adolescent Psychiatry, Psychosomatics and
> >>> Psychotherapy
> >>> University Hospital Frankfurt, Goethe University Frankfurt am Main,
> >>> Germany
> >>>
> >>> _______________________________________________
> >>> Freesurfer mailing list
> >>> 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 mailing list
> Freesurfer@nmr.mgh.harvard.edu
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychother
apy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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