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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