[Freesurfer] Comparing thickness at vertex level
Dear FreeSurfer experts,I'm wondering if is it possible to make vertex to vertex comparisons for thickness on a group of subjects. In other words, I have a bunch of subjects pre-processed with FS but I would like to make comparisons finding the thickness values at same vertex in all of them. Is this possible with Freesurfer?Given that at the beggining all they have different head/brain sizes, I was thinking that a regristration of the surfaces to the same space (FSaverage) would re-sample my data to match in number of vertex. for this, I think that maybe "mri_surf2surf" is capable of such a thing, and then I would have to search for each vertex, or optionally "mris_preproc" using the "-target FSaverage" flag would perform something similar. Please tell me what you think about this?Many thanks in advanced,Gabriel. ___ 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.
Re: [Freesurfer] Comparing thickness at vertex level
Hi Gabriel, this sounds like a standard surface-based thickness study. Or am I missing something? In case it is, you can look at the group analysis tutorial. Basically, you run mris_preproc (which puts all of your subjects into the fsaverage space and saves a stack of thickness maps in a single file), then you smooth it, then you run mri_glmfit. doug On 10/24/2012 11:47 AM, Gabriel Gonzalez Escamilla wrote: > > Dear FreeSurfer experts, > > I'm wondering if is it possible to make vertex to vertex comparisons > for thickness on a group of subjects. In other words, I have a bunch > of subjects pre-processed with FS but I would like to make comparisons > finding the thickness values at same vertex in all of them. Is this > possible with Freesurfer? > > Given that at the beggining all they have different head/brain sizes, > I was thinking that a regristration of the surfaces to the same space > (FSaverage) would re-sample my data to match in number of vertex. for > this, I think that maybe "mri_surf2surf" is capable of such a thing, > and then I would have to search for each vertex, or optionally > "mris_preproc" using the "-target FSaverage" flag ||*||*would perform > something similar. > > Please tell me what you think about this? > > > Many thanks in advanced, > Gabriel. > > > ___ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] Comparing thickness at vertex level
they will have the same number of vertices. They will all be in one file, and each vertex is a vertex in fsaverage space, which each subject vertex being mapped to the closest vertex in surface-based atlas. doug On 10/24/2012 04:34 PM, Gabriel Gonzalez Escamilla wrote: > Thanks Doug, > > Does the surface-based thickness approach make possible to compare > exactly the same vertex across all my subjects? or they will be still > have some differences in the number of vertices among them? > > Gabriel > > > El 24/10/12, *Douglas N Greve * escribió: >> Hi Gabriel, this sounds like a standard surface-based thickness study. >> Or am I missing something? In case it is, you can look at the group >> analysis tutorial. Basically, you run mris_preproc (which puts all of >> your subjects into the fsaverage space and saves a stack of thickness >> maps in a single file), then you smooth it, then you run mri_glmfit. >> >> doug >> >> On 10/24/2012 11:47 AM, Gabriel Gonzalez Escamilla wrote: >> > >> > Dear FreeSurfer experts, >> > >> > I'm wondering if is it possible to make vertex to vertex comparisons >> > for thickness on a group of subjects. In other words, I have a bunch >> > of subjects pre-processed with FS but I would like to make comparisons >> > finding the thickness values at same vertex in all of them. Is this >> > possible with Freesurfer? >> > >> > Given that at the beggining all they have different head/brain sizes, >> > I was thinking that a regristration of the surfaces to the same space >> > (FSaverage) would re-sample my data to match in number of vertex. for >> > this, I think that maybe "mri_surf2surf" is capable of such a thing, >> > and then I would have to search for each vertex, or optionally >> > "mris_preproc" using the "-target FSaverage" flag ||*||*would perform >> > something similar. >> > >> > Please tell me what you think about this? >> > >> > >> > Many thanks in advanced, >> > Gabriel. >> > >> > >> > ___ >> > 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 >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> ___ >> 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. >> > > -- > -- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggon...@upo.es > http://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
