[Freesurfer] Convert TAL coordinates to surface RAS coordinates

Dear experts, I have a set of Talairach coordinates that I want to convert to the individual subject surf RAS coordinates. How can I do this? Thank you very much. Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harv

Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

ig*inv(Torig) Thank you, ines On Fri, Dec 11, 2015 at 4:12 PM, Douglas Greve wrote: > > See if this helps > > https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > > On 12/11/15 10:23 AM, Inês Violante wrote: >> Dear experts, >> >> I have a set of T

Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

near the place where they were supposed to be, taking into account the projection of P4 to the cortex. Any ideas about what could be wrong? Thank you very much, ines On Fri, Dec 11, 2015 at 4:20 PM, Inês Violante wrote: > Dear Douglas, > > I've been looking a that page for a whil

[Freesurfer] MNI to Surf RAS problems

Hi, I am trying to convert MNI coordinates to a subject's anatomical space surf coordinates. While this MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' works fine from surf coordinates to MNI I don't know how to make it work correctly the other way around... i.e., knowing MNI305RAS and w

[Freesurfer] accuracy of cerebellar segmenation

Dear all, Does anyone have information on the accuracy of cerebellar segmenation into GM and WM? Thank you very much. ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inf

[Freesurfer] lobar WM volumes

Dear all, I need to obtain the white matter volume per lobe for a given numer of subjects. I started by using the following: mri_annotation2label --subject --hemi rh --lobesStrict lobe mri_aparc2aseg --s --labelwm --annot lobe and now I have a lobe+aseg.mgz file. How can I create a stats fil

[Freesurfer] lobar WM volumes

Dear all, I need to obtain the white matter volume per lobe for a given numer of subjects. I started by using the following: mri_annotation2label --subject --hemi rh --lobesStrict lobe mri_aparc2aseg --s --labelwm --annot lobe and now I have a lobe+aseg.mgz file.  How can I create a stats fil

Re: [Freesurfer] lobar WM volumes

is  will not have the numbers/names of your lobar regions, > so you'll need to create a new color table (or add to the one that is > there). > doug > > On 04/02/2012 12:58 PM, Inês Violante wrote: >> Dear all, >> >> I need to obtain the white matter volume per

[Freesurfer] lGI differences without variation in other cortical morphometric variables

Dear all, I am comparing a group of patients with controls. I extracted: cortical volume, surface area, cortical thickness and gyrification index for each subject's lobe. Comparisons between this variables with Total Intracranial Volume as a covariate indicated a difference in frontal and temporal

Re: [Freesurfer] lGI differences without variation in other cortical morphometric variables

Hi, Thank you so much for your reply. I am going to read the paper. However, if the increase in head size obscures the lGI, why this is not an overall variation? Meaning, why is only for the frontal and temporal lobes? thank you ines On Tue, May 15, 2012 at 4:30 PM, j janssen wrote: > Hi, >

[Freesurfer] average lGI for each subject's hemipshere

Dear all, How can I obtain an average lGI for each subject's hemipshere? I've tried: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh but I had the following error: ERROR: stating file .../label/lh.aparc.annot It cal

Re: [Freesurfer] average lGI for each subject's hemipshere

I think I got it, but it would be great if someone could tell me if this is wright: mris_anatomical_stats -l lh.cortex.label -t lh.pial_lgi -log file.txt SUBJECT lh pial thanks, ines On Tue, May 15, 2012 at 6:58 PM, Inês Violante wrote: > Dear all, > > How can I obtain an averag

[Freesurfer] Surface Area aparc from pial surface

Hi, I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that? Thank you a lot for your help. ines ___ Freesurfer mailing list Fre

Re: [Freesurfer] Surface Area aparc from pial surface

ent of mris_anatomical_stats allows you to specify the > surface to use (pial in your case) > > cheers, > -MH > > > NAME >        mris_anatomical_stats > > SYNOPSIS >        mris_anatomical_stats [options] > [] > > > On Fri, 2012-05-18 at 15:18 +0100, Inês Violante

Re: [Freesurfer] Surface Area aparc from pial surface

;> >> NAME >>          mris_anatomical_stats >> >> SYNOPSIS >>          mris_anatomical_stats [options]   >> [] >> >> >> On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote: >>> Hi, >>> >>> I need to know the surface area of the s

Re: [Freesurfer] Surface Area aparc from pial surface

: > Hi Ines, this is a good thing to post to the list since there are others > that might know better than me. Also, please include the  full terminal > output. > thanks > doug > > > > > On 05/18/2012 11:51 AM, Inês Violante wrote: >> >> Thanks a lot!