hi, not sure what you are trying to do, as the commands below seem to do what i expect them to do, which is to create a masked (skull-stripped) version of rawavg.mgz. what do you mean by 'manual segmentation changes'?, and what exactly is going wrong?

if you deleted voxels in brainmask.mgz, then perhaps you need to add the flag -keep_mask_deletion_edits to mri_mask to transfer those voxels ('deleted' voxels actually have a special value to indicate deleted).

n.

On Wed, 2011-03-09 at 22:28 +0000, Gabriel Go.Es. wrote:

Hello everybody, Sorry for the insistance, but I need to solve this...

I'm making some manual segmentation changes in the brainmask.mgz and using mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the output from the mri_vol2vol looks perfectly normal,and retains all changed made by me, but when I use the mri_mask command over the rawavg.mgz no segmentation seems to be donne in the final output file.

Does any one has an idea of what could be wrong?

the commands after manual corrections are:

mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz

Thanks in advanced, Gabriel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer