Hi Ajay
it's a surface file in our own (goofy) internal format. You can use
mris_info to dump the header, or read it into matlab if you like
cheers
Bruce
On Wed, 6 Apr 2016,
Ajay Kurani 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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