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Dear Freesurfer Developpers,
When I look at the FreeSurfer documentation on hippocampal segmentation, I see that it is possible to obtain different segmentations in addition to the 'traditionnal ' freesurfer 7 one: - HBT: the hippocampus is subdivided into head, body and tail. - FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e. there is no head/body subdivision for the hippocampus. no head/body subdivision for hippocampal sub-regions. - CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields.
When I run the command line: segmentHA_T1.sh bert I get files: hipposubfields.lh.T1.v21.stats which contain the volumes of the freesurfer 7 segmentation but not the other segmentations. I would like to generate a .stat file (one/subject) of segmentation type 'CA' , how can I do this?
Thank you, Best,
Yasmine
Hi Jasmine, This is tricky because the “absorption” happens at the discrete segmentation level (rather than using the soft probabilities). At that point, you’re probably better off counting voxels and multiplying by their volume. Doug: is there a way to do this with FreeSurfer programs, as opposed to using eg Matlab or Python? If not, you could run something like this in Matlab: addpath /path/to/freesurfer/matlab; mri = MRIread(segmentation_file); volume = sum(mri.vol(:)==label_of_interest) * det(mri.vox2ras0) Cheers, /E
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yasmine Salman yasmine.salman@uclouvain.be Date: Wednesday, October 18, 2023 at 5:22 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] HBT/FS60/CA segmentation
External Email - Use Caution Dear Freesurfer Developpers,
When I look at the FreeSurfer documentation on hippocampal segmentation, I see that it is possible to obtain different segmentations in addition to the 'traditionnal ' freesurfer 7 one: - HBT: the hippocampus is subdivided into head, body and tail. - FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e. there is no head/body subdivision for the hippocampus. no head/body subdivision for hippocampal sub-regions. - CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields.
When I run the command line: segmentHA_T1.sh bert I get files: hipposubfields.lh.T1.v21.stats which contain the volumes of the freesurfer 7 segmentation but not the other segmentations. I would like to generate a .stat file (one/subject) of segmentation type 'CA' , how can I do this?
Thank you, Best,
Yasmine
You can use mri_segstats, eg, mri_segstats --seg seg.mgz --sum summary.txt If the seg.mgz has an embedded color table that lists all the segmentatons, then the names will appear in the summary. If you have such a color table you can pass it with --ctab
On 10/18/2023 10:34 AM, Iglesias Gonzalez, Juan E. wrote:
Hi Jasmine,
This is tricky because the “absorption” happens at the discrete segmentation level (rather than using the soft probabilities).
At that point, you’re probably better off counting voxels and multiplying by their volume.
Doug: is there a way to do this with FreeSurfer programs, as opposed to using eg Matlab or Python?
If not, you could run something like this in Matlab:
addpath /path/to/freesurfer/matlab; mri = MRIread(segmentation_file); volume = sum(mri.vol(:)==label_of_interest) * det(mri.vox2ras0)
Cheers,
/E
--
Juan Eugenio Iglesias
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yasmine Salman yasmine.salman@uclouvain.be *Date: *Wednesday, October 18, 2023 at 5:22 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] HBT/FS60/CA segmentation
* External Email - Use Caution *
Dear Freesurfer Developpers,
When I look at the FreeSurfer documentation on hippocampal segmentation, I see that it is possible to obtain different segmentations in addition to the 'traditionnal ' freesurfer 7 one:
HBT: the hippocampus is subdivided into head, body and tail.
FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e. there is
no head/body subdivision for the hippocampus.
no head/body subdivision for hippocampal sub-regions.
- CA: the "internal" labels (GC-ML-DG and molecular layer) are
absorbed by the CA subfields.
When I run the command line: segmentHA_T1.sh bert
I get files: hipposubfields.lh.T1.v21.stats which contain the volumes of the freesurfer 7 segmentation but not the other segmentations. I would like to generate a .stat file (one/subject) of segmentation type 'CA' , how can I do this?
Thank you,
Best,
Yasmine
External Email - Use Caution
That works, thank you !!
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas N. Greve dgreve@MGH.HARVARD.EDU Envoyé : mercredi 18 octobre 2023 17:16 À : Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@MGH.HARVARD.EDU; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] HBT/FS60/CA segmentation
You can use mri_segstats, eg, mri_segstats --seg seg.mgz --sum summary.txt If the seg.mgz has an embedded color table that lists all the segmentatons, then the names will appear in the summary. If you have such a color table you can pass it with --ctab
On 10/18/2023 10:34 AM, Iglesias Gonzalez, Juan E. wrote:
Hi Jasmine,
This is tricky because the “absorption” happens at the discrete segmentation level (rather than using the soft probabilities).
At that point, you’re probably better off counting voxels and multiplying by their volume.
Doug: is there a way to do this with FreeSurfer programs, as opposed to using eg Matlab or Python?
If not, you could run something like this in Matlab:
addpath /path/to/freesurfer/matlab; mri = MRIread(segmentation_file); volume = sum(mri.vol(:)==label_of_interest) * det(mri.vox2ras0)
Cheers,
/E
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1kP_O3R_bMOU2GmINgz5cz91y_QeYf2DBWla-yJOGwraSGR-...http://secure-web.cisco.com/1yDH36iNf5mwHkAytk6BSbB5YDUJmMpviqDjyvRfRFv-F2axx7r3Ba5NatvLYybRU0KZ4Cxb9c3ow-SyVa0jmVG1ZHCJwYl87-j8TN8twl60GUs7JCZejjYgQp7hxZ5WpIvk3qJQuIhtw7f7QGrznvHLo82fBzq6c-BUITqp_T4JNHyJZjcm06Y2sJkyUzS-GqC5K0BhpG1m3wGb-3Ij_a5XyVXK6VdIMaDFA9jOz4gBjTgS3QH-Y72rUTiQQNnbfNEsa-LN3mijJn_zCe8TrkLKVe7gQTeQ9KbYZu4_uE2XVD4fbgKsK313L9FCNweL0/http%3A%2F%2Fwww.jeiglesias.com%2F
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yasmine Salman yasmine.salman@uclouvain.bemailto:yasmine.salman@uclouvain.be Date: Wednesday, October 18, 2023 at 5:22 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] HBT/FS60/CA segmentation
External Email - Use Caution
Dear Freesurfer Developpers,
When I look at the FreeSurfer documentation on hippocampal segmentation, I see that it is possible to obtain different segmentations in addition to the 'traditionnal ' freesurfer 7 one:
- HBT: the hippocampus is subdivided into head, body and tail.
- FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e. there is no head/body subdivision for the hippocampus.
no head/body subdivision for hippocampal sub-regions.
- CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields.
When I run the command line: segmentHA_T1.sh bert
I get files: hipposubfields.lh.T1.v21.stats which contain the volumes of the freesurfer 7 segmentation but not the other segmentations. I would like to generate a .stat file (one/subject) of segmentation type 'CA' , how can I do this?
Thank you,
Best,
Yasmine
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Iglesias Gonzalez, Juan E. -
Yasmine Salman