Mishkin,
This will create what you want:
cd subj/label mri_annotation2label --subject subj \ --hemi lh \ --annotation aparc \ --seg lh.aparc.mgh
replacing subj and lh with appropriate.
then type:
mris_convert -c ./lh.aparc.mgh \ ../surf/lh.white \ lh.aparc.asc
and the output file (lh.aparc.asc) will have lines like this:
71586 -39.60123 -13.37572 -34.24242 1007.00000
which are:
vno X Y Z labelno
where labelno is found in $FREESURFER_HOME/FreeSurferColorLUT.txt, for instance 1007 is ctx-lh-fusiform
Nick
On Tue, 2009-04-07 at 17:00 -0400, Mishkin Derakhshan wrote:
Thanks. After reading up on the wiki it seems that a more general solution I'm loking for would be to somehow get the contents of ?h.aparc.annot into ascii form. I know mris_annotation2label will kind of do this, but it creates one file for every label. What I'm loooking for is a single file with n rows corresponding to the n vertices in ?h.pial, and then next to each one, a number representing what label it belongs to (or what value to look up in the LUT). can this be done somehow, or at the very least can I get the contents of ?h.*.annot into ascii format so I can manipulate things.
thanks, mishkin
On Tue, Apr 7, 2009 at 1:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mishkin,
yes, the ?h.cortex.label should be created for every subject that labels the cortical regions of the surface.
cheers, Bruce On Tue, 7 Apr 2009, Mishkin Derakhshan wrote:
Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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