Dear FS team,
I'm writing matlab code to obtain smaller parcellated regions of equal size starting from the freesurfer parcellation performed on the average subject. Should I apply a scale factor If I wanted to use the areas stored in ?h.white.avg.area.mgh for the new parcellation? My Freesurfer release is 4.2
Thanks in advance for your help.
Best, Rafa
The value at each vertex of ?h.white.avg.area.mgh is the average area at that vertex averaged over all the input subjects. Note that the area of a vertex in the average subject will likely be much less and is not particularly meaningful. I'm not sure if this answers your question or not..
doug
Rafa x wrote:
Dear FS team,
I'm writing matlab code to obtain smaller parcellated regions of equal size starting from the freesurfer parcellation performed on the average subject. Should I apply a scale factor If I wanted to use the areas stored in ?h.white.avg.area.mgh for the new parcellation? My Freesurfer release is 4.2
Thanks in advance for your help.
Best, Rafa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Rafa,
Not sure if this will help, but Bruce recently created a utility to generate a parcellation based on which icosahedral face each vertex maps to. Its called mris_make_face_parcellation, and you can get it here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/
ex.: cd <subj>/surf mris_make_face_parcellation \ lh.inflated \ $FREESURFER_HOME/lib/bem/ic3.tri \ lh.ic3.annot
then:
tksurfer <subj> lh inflated -annotation ic3
there are other 'ic' files in that bem dir to try, to give you different number of faces.
Nick
On Thu, 2009-02-26 at 11:39 +0100, Rafa x wrote:
Dear FS team,
I'm writing matlab code to obtain smaller parcellated regions of equal size starting from the freesurfer parcellation performed on the average subject. Should I apply a scale factor If I wanted to use the areas stored in ?h.white.avg.area.mgh for the new parcellation? My Freesurfer release is 4.2
Thanks in advance for your help.
Best, Rafa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug and Nick,
In my matlab code when I sum the area stored in ?h.white.avg.area.mgh I obtain an area of 82219 mm. Are these area values affected by the problem explained in http://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface? Have I to multiply the values for 1.2? Nick, thank you for your idea but I'm writing a new program because I need a regions with the same area and (here is the difference) this new regions need to by a subregion of the originial freesurfer parcellation (for preserve the anatomical division).
Thank you for your response,
Rafa
2009/2/26 Nick Schmansky nicks@nmr.mgh.harvard.edu:
Rafa,
Not sure if this will help, but Bruce recently created a utility to generate a parcellation based on which icosahedral face each vertex maps to. Its called mris_make_face_parcellation, and you can get it here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/
ex.: cd <subj>/surf mris_make_face_parcellation \ lh.inflated \ $FREESURFER_HOME/lib/bem/ic3.tri \ lh.ic3.annot
then:
tksurfer <subj> lh inflated -annotation ic3
there are other 'ic' files in that bem dir to try, to give you different number of faces.
Nick
On Thu, 2009-02-26 at 11:39 +0100, Rafa x wrote:
Dear FS team,
I'm writing matlab code to obtain smaller parcellated regions of equal size starting from the freesurfer parcellation performed on the average subject. Should I apply a scale factor If I wanted to use the areas stored in ?h.white.avg.area.mgh for the new parcellation? My Freesurfer release is 4.2
Thanks in advance for your help.
Best, Rafa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu