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

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