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.kurani@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