Hello experts,
I identified two clusters (X for thickness and Y for volume) showing significant association between cortical measures (thickness and volume) and motor-performance. I followed steps from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and got several output files same as mentioned at the bottom of this page i.e. cache*.*
I am interested in getting subject-wise thickness and volume values from these two clusters X and Y.
From previous posts, I found that these subjectwise cluster values (e.g.
thickness and volume) are saved in *.ocn.dat file. If that's correct, I have following questions:
(1). When I look at *.ocn.dat file, subjectwise thickness values range between 2-3 and volume values are in the range between 0-2. I am not sure if that makes sense and what are the units of thickness and volume here?
(2). Since *.ocn.dat file for X gives subjectwise thickness value for cluster X and *.ocn.dat file for Y gives subjectwise volume values for cluster Y, so how can I get volume values for cluster X and thickness values for cluster Y?
From pervious FS discussion, I found that it can be done using *.ocn.annot
files e.g. to extract volume values from X, *.ocn.annot for X can be used in mris_anatomical_stats file. To make sure and confirm that this is the correct approach, I calculated thickness values for X using this approach, expecting that these should match with *.ocn.dat for X but it's not matching. I also converted *.annot to *.label in native space following steps from https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html but still values are not matching with *.ocn.dat.
I would really appreciate any help.
Thanks, Sahil
Hello everyone,
I was wondering if someone could please help me in figuring out following issues.
Thanks a lot, Sahil ---------- Forwarded message ---------- From: Sahil Bajaj sahil.brain@gmail.com Date: Thu, Feb 15, 2018 at 3:50 PM Subject: Subjectwise extraction from ROIs To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello experts,
I identified two clusters (X for thickness and Y for volume) showing significant association between cortical measures (thickness and volume) and motor-performance. I followed steps from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and got several output files same as mentioned at the bottom of this page i.e. cache*.*
I am interested in getting subject-wise thickness and volume values from these two clusters X and Y.
From previous posts, I found that these subjectwise cluster values (e.g.
thickness and volume) are saved in *.ocn.dat file. If that's correct, I have following questions:
(1). When I look at *.ocn.dat file, subjectwise thickness values range between 2-3 and volume values are in the range between 0-2. I am not sure if that makes sense and what are the units of thickness and volume here?
(2). Since *.ocn.dat file for X gives subjectwise thickness value for cluster X and *.ocn.dat file for Y gives subjectwise volume values for cluster Y, so how can I get volume values for cluster X and thickness values for cluster Y?
From pervious FS discussion, I found that it can be done using *.ocn.annot
files e.g. to extract volume values from X, *.ocn.annot for X can be used in mris_anatomical_stats file. To make sure and confirm that this is the correct approach, I calculated thickness values for X using this approach, expecting that these should match with *.ocn.dat for X but it's not matching. I also converted *.annot to *.label in native space following steps from https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html but still values are not matching with *.ocn.dat.
I would really appreciate any help.
Thanks, Sahil
sorry for the delay, thanks for reposting
On 02/20/2018 11:33 AM, Sahil Bajaj wrote:
Hello everyone,
I was wondering if someone could please help me in figuring out following issues.
Thanks a lot, Sahil ---------- Forwarded message ---------- From: *Sahil Bajaj* <sahil.brain@gmail.com mailto:sahil.brain@gmail.com> Date: Thu, Feb 15, 2018 at 3:50 PM Subject: Subjectwise extraction from ROIs To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hello experts,
I identified two clusters (X for thickness and Y for volume) showing significant association between cortical measures (thickness and volume) and motor-performance. I followed steps from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and got several output files same as mentioned at the bottom of this page i.e. cache*.*
I am interested in getting subject-wise thickness and volume values from these two clusters X and Y.
From previous posts, I found that these subjectwise cluster values (e.g. thickness and volume) are saved in *.ocn.dat file. If that's correct, I have following questions:
(1). When I look at *.ocn.dat file, subjectwise thickness values range between 2-3 and volume values are in the range between 0-2. I am not sure if that makes sense and what are the units of thickness and volume here?
Thickness is mm and the value is mean thickness, so that makes sense. Volume is mm3, and the value is "mean" volume, which makes less sense. You can multiply the mean volume by the number of vertices to get total volume.
(2). Since *.ocn.dat file for X gives subjectwise thickness value for cluster X and *.ocn.dat file for Y gives subjectwise volume values for cluster Y, so how can I get volume values for cluster X and thickness values for cluster Y?
Assuming that they are different cluster maps, you can run mri_segstats --seg thicknessglm/contrast/csdbase.sig.ocn.mgh --exclude 0 --i volumestack.mgh --avgwf volume.thickness-clusters.dat --sum deleteme.sum where volumestack would be the input to the volume-based glm.
From pervious FS discussion, I found that it can be done using *.ocn.annot files e.g. to extract volume values from X, *.ocn.annot for X can be used in mris_anatomical_stats file. To make sure and confirm that this is the correct approach, I calculated thickness values for X using this approach, expecting that these should match with *.ocn.dat for X but it's not matching. I also converted *.annot to *.label in native space following steps from https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html but still values are not matching with *.ocn.dat.
Use the mri_segstats command above
I would really appreciate any help.
Thanks, Sahil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Dr. Greve,
I have following follow-up questions ('red' colored) for you and would really appreciate any help.
On Tue, Feb 20, 2018 at 2:59 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
sorry for the delay, thanks for reposting
On 02/20/2018 11:33 AM, Sahil Bajaj wrote:
Hello everyone,
I was wondering if someone could please help me in figuring out following issues.
Thanks a lot, Sahil ---------- Forwarded message ---------- From: *Sahil Bajaj* <sahil.brain@gmail.com <mailto:sahil.brain@gmail.com
Date: Thu, Feb 15, 2018 at 3:50 PM Subject: Subjectwise extraction from ROIs To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hello experts,
I identified two clusters (X for thickness and Y for volume) showing significant association between cortical measures (thickness and volume) and motor-performance. I followed steps from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and got several output files same as mentioned at the bottom of this page i.e. cache*.*
I am interested in getting subject-wise thickness and volume values from these two clusters X and Y.
From previous posts, I found that these subjectwise cluster values (e.g. thickness and volume) are saved in *.ocn.dat file. If that's correct, I have following questions:
(1). When I look at *.ocn.dat file, subjectwise thickness values range between 2-3 and volume values are in the range between 0-2. I am not sure if that makes sense and what are the units of thickness and volume here?
Thickness is mm and the value is mean thickness, so that makes sense. Volume is mm3, and the value is "mean" volume, which makes less sense. You can multiply the mean volume by the number of vertices to get total volume.
Thanks for the clarification Dr. Greve. Could you please tell me how can I find number of vertices for each cluster (subjectwise) so that I can multiple that with mean volume values.
(2). Since *.ocn.dat file for X gives subjectwise thickness value for cluster X and *.ocn.dat file for Y gives subjectwise volume values for cluster Y, so how can I get volume values for cluster X and thickness values for cluster Y?
Assuming that they are different cluster maps, you can run mri_segstats --seg thicknessglm/contrast/csdbase.sig.ocn.mgh --exclude 0 --i volumestack.mgh --avgwf volume.thickness-clusters.dat --sum deleteme.sum where volumestack would be the input to the volume-based glm.
Just to confirm volumestack is the file (lh.X_vol.10.mgh) generated after following steps, correct? mris_preproc --fsgd X.fsgd --target fsaverage --hemi lh --meas volume --out X/lh.X_vol.mgh mri_surf2surf --hemi lh --s fsaverage --sval X/lh.X_vol.mgh --fwhm 10 --cortex --tval X/lh.X_vol.10.mgh
Could you please confirm if that's correct? If that's correct, then mri_segstats command as you described above gives mean volume values again, so again I need number of vertices here and I am not sure how to get number of vertices for corresponding clusters.
Thanks a lot. Sahil
From pervious FS discussion, I found that it can be done using *.ocn.annot files e.g. to extract volume values from X, *.ocn.annot for X can be used in mris_anatomical_stats file. To make sure and confirm that this is the correct approach, I calculated thickness values for X using this approach, expecting that these should match with *.ocn.dat for X but it's not matching. I also converted *.annot to *.label in native space following steps from https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/
msg53591.html
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
/msg53591.html>
but still values are not matching with *.ocn.dat.
Use the mri_segstats command above
I would really appreciate any help.
Thanks, Sahil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
On 02/20/2018 05:54 PM, Sahil Bajaj wrote:
Dear Dr. Greve,
I have following follow-up questions ('red' colored) for you and would really appreciate any help.
On Tue, Feb 20, 2018 at 2:59 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
sorry for the delay, thanks for reposting On 02/20/2018 11:33 AM, Sahil Bajaj wrote: > Hello everyone, > > I was wondering if someone could please help me in figuring out > following issues. > > Thanks a lot, > Sahil > ---------- Forwarded message ---------- > From: *Sahil Bajaj* <sahil.brain@gmail.com <mailto:sahil.brain@gmail.com> <mailto:sahil.brain@gmail.com <mailto:sahil.brain@gmail.com>>> > Date: Thu, Feb 15, 2018 at 3:50 PM > Subject: Subjectwise extraction from ROIs > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Hello experts, > > I identified two clusters (X for thickness and Y for volume) showing > significant association between cortical measures (thickness and > volume) and motor-performance. I followed steps from here: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > and got several output files same as mentioned at the bottom of this > page i.e. cache*.* > > I am interested in getting subject-wise thickness and volume values > from these two clusters X and Y. > > From previous posts, I found that these subjectwise cluster values > (e.g. thickness and volume) are saved in *.ocn.dat file. If that's > correct, I have following questions: > > (1). When I look at *.ocn.dat file, subjectwise thickness values range > between 2-3 and volume values are in the range between 0-2. I am not > sure if that makes sense and what are the units of thickness and > volume here? Thickness is mm and the value is mean thickness, so that makes sense. Volume is mm3, and the value is "mean" volume, which makes less sense. You can multiply the mean volume by the number of vertices to get total volume.Thanks for the clarification Dr. Greve. Could you please tell me how can I find number of vertices for each cluster (subjectwise) so that I can multiple that with mean volume values.
This will be in the csdbase.sig.cluster.summary file.
> > (2). Since *.ocn.dat file for X gives subjectwise thickness value for > cluster X and *.ocn.dat file for Y gives subjectwise volume values for > cluster Y, so how can I get volume values for cluster X and thickness > values for cluster Y? Assuming that they are different cluster maps, you can run mri_segstats --seg thicknessglm/contrast/csdbase.sig.ocn.mgh --exclude 0 --i volumestack.mgh --avgwf volume.thickness-clusters.dat --sum deleteme.sum where volumestack would be the input to the volume-based glm.Just to confirm volumestack is the file (lh.X_vol.10.mgh) generated after following steps, correct? mris_preproc --fsgd X.fsgd --target fsaverage --hemi lh --meas volume --out X/lh.X_vol.mgh mri_surf2surf --hemi lh --s fsaverage --sval X/lh.X_vol.mgh --fwhm 10 --cortex --tval X/lh.X_vol.10.mgh
Could you please confirm if that's correct?
Yes.
If that's correct, then mri_segstats command as you described above gives mean volume values again, so again I need number of vertices here and I am not sure how to get number of vertices for corresponding clusters.
You can get them from the above. In this case, you can also add --accumulate to the mri_segstats command line
Thanks a lot. Sahil
> > From pervious FS discussion, I found that it can be done using > *.ocn.annot files e.g. to extract volume values from X, *.ocn.annot > for X can be used in mris_anatomical_stats file. To make sure and > confirm that this is the correct approach, I calculated thickness > values for X using this approach, expecting that these should match > with *.ocn.dat for X but it's not matching. > I also converted *.annot to *.label in native space following steps > from > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html> > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html>> > but still values are not matching with *.ocn.dat. Use the mri_segstats command above > > I would really appreciate any help. > > Thanks, > Sahil > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Sahil Bajaj