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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