glad it worked out
Bruce
On Wed, 22 Jan 2020, Tim Schäfer wrote:
External Email - Use Caution
Hi Antonin and Bruce,
thanks for your great suggestions and the headsup on the command line history
in the file. I tried both methods and they both work.
We will definitely remove the IDs, so this is very helpful.
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
On January 21, 2020 at 11:02 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
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
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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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