For 1., you can try:

mri_concat --combine \ --i rh.pialvol.mgz \ --i lh.pialvol.mgz \ --o pialvol.mgz

where in this example, rh.pialvol.mgz and lh.pialvol.mgz are outputs from the mris_fill run.

You may want to include the -c flag when running mris_fill, to create output vols of dimension 256^3.

Nick

On Thu, 2008-05-22 at 17:23 -0500, Cochrane Jamison wrote:

I am using mris_fill to create a volume from the lh.pial surface as well as the rh.pial surface. I have 2 questions:

 1. How can I combine the 2 separate hemisphere volumes into a
    single full brain volume that I can export and view in
    analyze?  I only know to use mri_convert on each one
    separately.  Does this need to be done before I run mris_fill,
    or is there another combined surface that has the same
    resolution as the pial surfaces that I can run mris_fill on?
 2. I know that when I run mris_fill, the volumes that are
    produced do not contain orientation information.  When I load
    them into Analyze, the volume is mirrored and upside down.  I
    was wondering how I can “get” orientation information back
    into the volume, and also correct the mirrored and upside down
    viewing issue.  

These results were produced by Freesurfer from standard dicom files from a volumetric scan.

Thanks,

Cochrane Jamison

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