External Email - Use Caution
Dear FreeSurfer experts,
I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per surface vertex.)
I have already done the same for the white surfaces, and it was pretty straight-forward: 1) Save the per-vertex data in a curv-format file in SUBJECTS_DIR/<subject>/surf/?h.<measure> 2) Run 'recon-all -s <subject> -qcache -measure <measure>'
This will map the data to fsaverage and create files named ?h.<measure>.fwhm<n>.fsaverage.mgh in the surf/ directories as expected (where <n> is 0, 5, .., 25).
My question is: how can I do the same for my data from the pial surface? Are there any command line options for 'recon-all' (or maybe for mris_preproc) that can do this?
I already tried to put the pial per-vertex data into files named SUBJECTS_DIR/<subject>/surf/?h.pial.<measure>, but they are not handled by the recon-all command listed above: no fsaverage files show up for them.
Thanks in advance,
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
You can use preproc-sess and specify the --meas flag. Run with --help for more info.
On 10/18/18 2:08 PM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear FreeSurfer experts,
I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per surface vertex.)
I have already done the same for the white surfaces, and it was pretty straight-forward:
- Save the per-vertex data in a curv-format file in SUBJECTS_DIR/<subject>/surf/?h.<measure>
- Run 'recon-all -s <subject> -qcache -measure <measure>'
This will map the data to fsaverage and create files named ?h.<measure>.fwhm<n>.fsaverage.mgh in the surf/ directories as expected (where <n> is 0, 5, .., 25).
My question is: how can I do the same for my data from the pial surface? Are there any command line options for 'recon-all' (or maybe for mris_preproc) that can do this?
I already tried to put the pial per-vertex data into files named SUBJECTS_DIR/<subject>/surf/?h.pial.<measure>, but they are not handled by the recon-all command listed above: no fsaverage files show up for them.
Thanks in advance,
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
External Email - Use Caution
Dear Douglas,
thanks for your answer.
Did you by any chance mean mris_preproc instead of preproc-sess? The latter seems to have no --meas flag according to the help (and a quick grep through the script file).
I ended up placing the curv files in /surf/?h.<measure>.pial and the running: recon-all -s $SUBJECT -qcache -no-isrunning -measure ${MEASURE}.pial
This seems to also have done the trick, and it seems to be the way it is done by recon-all for the area.
I only expected that you have to explicitly define that the values should be mapped to the pial surface of the fsaverage subject. But if vertex #n in the pial is the closest vertex to vertex #n in the white, maybe no special handling is needed?
Tim
On October 23, 2018 at 6:08 PM "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
You can use preproc-sess and specify the --meas flag. Run with --help for more info.
On 10/18/18 2:08 PM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear FreeSurfer experts,
I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per surface vertex.)
I have already done the same for the white surfaces, and it was pretty straight-forward:
- Save the per-vertex data in a curv-format file in SUBJECTS_DIR/<subject>/surf/?h.<measure>
- Run 'recon-all -s <subject> -qcache -measure <measure>'
This will map the data to fsaverage and create files named ?h.<measure>.fwhm<n>.fsaverage.mgh in the surf/ directories as expected (where <n> is 0, 5, .., 25).
My question is: how can I do the same for my data from the pial surface? Are there any command line options for 'recon-all' (or maybe for mris_preproc) that can do this?
I already tried to put the pial per-vertex data into files named SUBJECTS_DIR/<subject>/surf/?h.pial.<measure>, but they are not handled by the recon-all command listed above: no fsaverage files show up for them.
Thanks in advance,
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
-- 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 10/25/2018 11:31 AM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear Douglas,
thanks for your answer.
Did you by any chance mean mris_preproc instead of preproc-sess? The latter seems to have no --meas flag according to the help (and a quick grep through the script file).
Yes, sorry.
I ended up placing the curv files in /surf/?h.<measure>.pial and the running: recon-all -s $SUBJECT -qcache -no-isrunning -measure ${MEASURE}.pial
This seems to also have done the trick, and it seems to be the way it is done by recon-all for the area.
That should work, but you should have been able to use mris_preproc directly (recon-all just calls mris_preproc).
I only expected that you have to explicitly define that the values should be mapped to the pial surface of the fsaverage subject. But if vertex #n in the pial is the closest vertex to vertex #n in the white, maybe no special handling is needed?
Right, the white and the pail use the same registratin
Tim
On October 23, 2018 at 6:08 PM "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
You can use preproc-sess and specify the --meas flag. Run with --help for more info.
On 10/18/18 2:08 PM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear FreeSurfer experts,
I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per surface vertex.)
I have already done the same for the white surfaces, and it was pretty straight-forward:
- Save the per-vertex data in a curv-format file in SUBJECTS_DIR/<subject>/surf/?h.<measure>
- Run 'recon-all -s <subject> -qcache -measure <measure>'
This will map the data to fsaverage and create files named ?h.<measure>.fwhm<n>.fsaverage.mgh in the surf/ directories as expected (where <n> is 0, 5, .., 25).
My question is: how can I do the same for my data from the pial surface? Are there any command line options for 'recon-all' (or maybe for mris_preproc) that can do this?
I already tried to put the pial per-vertex data into files named SUBJECTS_DIR/<subject>/surf/?h.pial.<measure>, but they are not handled by the recon-all command listed above: no fsaverage files show up for them.
Thanks in advance,
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
-- 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
External Email - Use Caution
Thanks for your time and the clarification.
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 November 7, 2018 at 3:28 PM "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
On 10/25/2018 11:31 AM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear Douglas,
thanks for your answer.
Did you by any chance mean mris_preproc instead of preproc-sess? The latter seems to have no --meas flag according to the help (and a quick grep through the script file).
Yes, sorry.
I ended up placing the curv files in /surf/?h.<measure>.pial and the running: recon-all -s $SUBJECT -qcache -no-isrunning -measure ${MEASURE}.pial
This seems to also have done the trick, and it seems to be the way it is done by recon-all for the area.
That should work, but you should have been able to use mris_preproc directly (recon-all just calls mris_preproc).
I only expected that you have to explicitly define that the values should be mapped to the pial surface of the fsaverage subject. But if vertex #n in the pial is the closest vertex to vertex #n in the white, maybe no special handling is needed?
Right, the white and the pail use the same registratin
Tim
On October 23, 2018 at 6:08 PM "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
You can use preproc-sess and specify the --meas flag. Run with --help for more info.
On 10/18/18 2:08 PM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear FreeSurfer experts,
I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per surface vertex.)
I have already done the same for the white surfaces, and it was pretty straight-forward:
- Save the per-vertex data in a curv-format file in SUBJECTS_DIR/<subject>/surf/?h.<measure>
- Run 'recon-all -s <subject> -qcache -measure <measure>'
This will map the data to fsaverage and create files named ?h.<measure>.fwhm<n>.fsaverage.mgh in the surf/ directories as expected (where <n> is 0, 5, .., 25).
My question is: how can I do the same for my data from the pial surface? Are there any command line options for 'recon-all' (or maybe for mris_preproc) that can do this?
I already tried to put the pial per-vertex data into files named SUBJECTS_DIR/<subject>/surf/?h.pial.<measure>, but they are not handled by the recon-all command listed above: no fsaverage files show up for them.
Thanks in advance,
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
-- 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@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
ts+ml＠rcmd.org