mri_mc uses marching cubes to build a tessellation, which mri_tesselate
puts vertices on the corners of every voxel face that is a border between
"on" and "off" voxels
cheers
Bruce
On
Wed, 30 Nov 2011, Douglas N Greve wrote:
> Hi Jie, what do you mean they don't work? I don't know what the
> d
Hi Jie, what do you mean they don't work? I don't know what the
difference between mri_mc and mri_tesselate is (another good reason to
post to the list so that others who might know can answer the question).
doug
Jie Shi wrote:
> Sorry I have forgot to describe our surface format.
>
> Vertex 1 x
yes, that has the subcortical segmentation based on the automatic
algorithm and any changes that you might have made manually. The "auto"
is only the result from the automatic method.
doug
Jie Shi wrote:
> Thanks a lot. Will try. Basically, is aseg.mgz the resulting file
> which contains the re
cd $SUBJECTS_DIR/subject/surf
mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates a
surface with jagged edges
mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # smooths
surface 10 smoothing steps is just a guess
# Visusalize the surface
tksurfer subject lh hippocampus.sm1
You can extract a binary mask for any structure with
mri_binarize --i aseg.mgz --match XX --o yourmask.mgh
where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt (eg,
17 = left hippo)
It is possible to generate hippo surfaces, but we cannot guarantee
accuracy. Let me know if you want t
Hi, experts. We need to use FreeSurfer to process some analyze image data.
More specifically, we want to extract the hippocampus surfaces. We know
that FreeSurfer has done subcortical segmentation during -autorecon2 stage
in recon-all. We have checked the resulting aseg.mgz file and found that it
c
