External Email - Use Caution
Hi, Tim,
the subject ID can be also contained in the commandline history which is stored 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 contain 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 CautionHi Douglas,
sure, you can get two example files here:
wget http://rcmd.org/tmp/brain.mgz wget http://rcmd.org/tmp/lh.BA1_exvivo.labelThe 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 by:
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 talairThe second file is an ASCII label from the same subject. You can get the ID by running:
head -n 1 lh.BA1_exvivo.labelThere are some other files which contain the ID, these are just 2 examples.
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 files 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 CautionDear FreeSurfer experts,
I have two questions on subject IDs in FreeSurfer output.
- 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 contain 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?
- 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 because 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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 CautionHi Douglas,
sure, you can get two example files here:
wget http://rcmd.org/tmp/brain.mgz wget http://rcmd.org/tmp/lh.BA1_exvivo.labelThe 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 talairThe second file is an ASCII label from the same subject. You can get the
ID
by running:
head -n 1 lh.BA1_exvivo.labelThere 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 CautionDear FreeSurfer experts,
I have two questions on subject IDs in FreeSurfer output.
- 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?
- 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
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 fischl@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 CautionHi Douglas,
sure, you can get two example files here:
wget http://rcmd.org/tmp/brain.mgz wget http://rcmd.org/tmp/lh.BA1_exvivo.labelThe 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 talairThe second file is an ASCII label from the same subject. You can get the
ID
by running:
head -n 1 lh.BA1_exvivo.labelThere 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 CautionDear FreeSurfer experts,
I have two questions on subject IDs in FreeSurfer output.
- 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?
- 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
glad it worked out Bruce On Wed, 22 Jan 2020, Tim Schäfer wrote:
External Email - Use CautionHi 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 fischl@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 CautionHi Douglas,
sure, you can get two example files here:
wget http://rcmd.org/tmp/brain.mgz wget http://rcmd.org/tmp/lh.BA1_exvivo.labelThe 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 talairThe second file is an ASCII label from the same subject. You can get the
ID
by running:
head -n 1 lh.BA1_exvivo.labelThere 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
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@nmr.mgh.harvard.edu
-
Antonin Skoch -
Bruce Fischl -
Tim Schäfer