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 <fis...@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 > >> > >> > >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer