Hi Ajay
.mgh file doesn't store the necessary topological informations
(neighbors, faces, and such) to store a surface. You can convert to gifti
and some other modeling formats (or ascii)
cheers
Bruce
On Wed, 6 Apr 2016, Ajay Kurani wrote:
Thanks for clarifying Bruce.
Just curious is there any freesurfer commands to convert this internal
surface file into a .mgh file for external use? For example mri_surf2vol or
mri_surf2label etc?
Thanks,
Ajay
On Wed, Apr 6, 2016 at 5:17 PM, Ajay Kurani <dr.ajay.kur...@gmail.com>
wrote:
Hello Freesurfer Experts,
I ran the following commands (from recon-all devtable) to create a
surface model of the ROI's that I am interested in (they start off as
a binary 1 mask):
1) mri_tesselate ../mri/lh.ROI.mgz 1 ../surf/lh.orig.nofix
2) mris_extract_main_component ../surf/lh.orig.nofix
../surf/lh.orig.nofix
3) mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix
../surf/lh.smooth.nofix
4) mris_inflate
5) mris_sphere
6) mri_fixtopology
When I use freeview the lh.smooth.nofix looks great. I wanted to use
this file to create a surface and volume file, however mri_info
lh.smooth.nofix comes up with the error of unknown filetype.
What is the lh.smooth.nofix filetype?
How would i be able to convert this lh.smooth.nofix to be used as a
surface for surface-based analysis? Are there other files that need
to be created first in order to convert this file to a surface? Is
this file a label, annotation surface etc?
Thanks,
Ajay
On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani
<dr.ajay.kur...@gmail.com> wrote:
Hi Freesurfer experts, I wanted to create a Freesurfer
surface on some of the aseg ROIs. I was able to run
mri_tesselate, mris_smooth, mris_inflate and mris_sphere
some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted
to run mris_fix_topology to fix this issue. In trying to run
this command it appears that mris_fix_topology tries to correct
based off of a brain sphere (which this ROI is clearly not) and
therefore it fails. I plan to then run subsequent steps such as
mris_euler number and mris_remove_intersections
1) Is there any way to fix the topology of this ROI using
freesurfer tools or a way to work around this issue? Do you
feel the sphere is needed for a small subcortical surface (ie
globus pallidus) or is this really more for complex structures
such as cortical surfaces?
2) Is there a recommended set of steps to accomplish creating a
surface from the ROI that is different from what I stated?
Thanks,
Ajay
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