Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ Cannot calloc()
Would this be because my input data is not compatible with the mri_tessellate command?
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to create the surface, then introduce the cut(s) and run mris_flatten -1 on the resulting patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't terribly well documented. You need the -1 flag to tell it to only use that one surface that you are giving it, and not to assume that the entire FS directory structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some advice
how to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if
not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain
area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense
to
flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain region)
and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer
some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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