Dear all,
I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region?
Best, Martijn
I would use mri_segstats and specify the --annot option doug
On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
Dear all,
I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region?
Best, Martijn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0).
Any thoughts?
On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
I would use mri_segstats and specify the --annot option doug
On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
Dear all,
I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region?
Best, Martijn
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/
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It can do both. When you spec --annot, then it does it on the surface and you have to pass it surface data (which you already have since you ran vol2surf). doug
On 05/28/2013 02:03 PM, Martijn Steenwijk wrote:
Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0).
Any thoughts?
On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: > Dear all, > > I've created a custom '.mgh' file containing values on the cortical > surface using mri_vol2surf. I would like to compute some statistics on > this surface in the aparc-areas computed by freesurfer. Can I then > just use mri_anatomical_stats with option -t specifying the custom > mgh file as 'thickness' input? Or does mri_anatomical_stats something > more complex than just averaging the values inside each region? > > Best, > Martijn > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats.
I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this?
Best, Martijn
On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk < martijnsteenwijk@gmail.com> wrote:
Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0).
Any thoughts?
On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
I would use mri_segstats and specify the --annot option doug
On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
Dear all,
I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region?
Best, Martijn
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.
what do you mean? That the vertices are not uniform? mri_segstats just computes the mean over the parcellation without reference to non-uniformity. doug
On 05/28/2013 02:15 PM, Martijn Steenwijk wrote:
Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats.
I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this?
Best, Martijn
On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk <martijnsteenwijk@gmail.com mailto:martijnsteenwijk@gmail.com> wrote:
Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: > Dear all, > > I've created a custom '.mgh' file containing values on the cortical > surface using mri_vol2surf. I would like to compute some statistics on > this surface in the aparc-areas computed by freesurfer. Can I then > just use mri_anatomical_stats with option -t specifying the custom > mgh file as 'thickness' input? Or does mri_anatomical_stats something > more complex than just averaging the values inside each region? > > Best, > Martijn > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
I mean; if you devide the number of vertices by the area per aparc-parcellation, some parcellations have relatively more vertices per mm^2 as others. If you now would compute the average thickness in for example the lobe-parcellation, the thicknesses of some areas (the parcellations with relatively more vertices per mm^2) get a higher weight in the overal average. Is that true?
On Tue, May 28, 2013 at 8:58 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
what do you mean? That the vertices are not uniform? mri_segstats just computes the mean over the parcellation without reference to non-uniformity. doug
On 05/28/2013 02:15 PM, Martijn Steenwijk wrote:
Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats.
I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this?
Best, Martijn
On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk < martijnsteenwijk@gmail.com <mailto:martijnsteenwijk@**gmail.commartijnsteenwijk@gmail.com>> wrote:
Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote:
I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: > Dear all, > > I've created a custom '.mgh' file containing values on the cortical > surface using mri_vol2surf. I would like to compute some statistics on > this surface in the aparc-areas computed by freesurfer. Can I then > just use mri_anatomical_stats with option -t specifying the custom > mgh file as 'thickness' input? Or does mri_anatomical_stats something > more complex than just averaging the values inside each region? > > Best, > Martijn > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<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<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> <http://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> <http://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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
I think it depends on how you do the computation. You would probably weight each vertex by the area then sum then divide by the total area and this is probably not much different than just averaging over vertices without taking the area into account. doug
On 5/29/13 9:16 AM, Martijn Steenwijk wrote:
I mean; if you devide the number of vertices by the area per aparc-parcellation, some parcellations have relatively more vertices per mm^2 as others. If you now would compute the average thickness in for example the lobe-parcellation, the thicknesses of some areas (the parcellations with relatively more vertices per mm^2) get a higher weight in the overal average. Is that true?
On Tue, May 28, 2013 at 8:58 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what do you mean? That the vertices are not uniform? mri_segstats just computes the mean over the parcellation without reference to non-uniformity. doug On 05/28/2013 02:15 PM, Martijn Steenwijk wrote: Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats. I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this? Best, Martijn On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk <martijnsteenwijk@gmail.com <mailto:martijnsteenwijk@gmail.com> <mailto:martijnsteenwijk@gmail.com <mailto:martijnsteenwijk@gmail.com>>> wrote: Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: > Dear all, > > I've created a custom '.mgh' file containing values on the cortical > surface using mri_vol2surf. I would like to compute some statistics on > this surface in the aparc-areas computed by freesurfer. Can I then > just use mri_anatomical_stats with option -t specifying the custom > mgh file as 'thickness' input? Or does mri_anatomical_stats something > more complex than just averaging the values inside each region? > > Best, > Martijn > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: 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> <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- 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 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/
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve
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Martijn Steenwijk