Hi,
I'm not sure whether the --seg option ever got looked into, but for
those searching the lists in the future, here is the quick hack I used
in perl to accomplish what I wanted:
mishkin
#! /usr/bin/perl
if($ARGV <1){
print "\nUsage: $0 \n";
print "Assumes SUBJECTS_DIR is set, and mri_a
Hi Nick,
I was recently trying to redo something you had helped me out with
back in April (see below), but I now get this error:
ERROR: Option --seg unknown
The wiki page still says this option exists, but I'm guessing is outdated
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label#Deta
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 (l
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
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 surfa
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
