mris_fill is an auxiliary tool that isn't part of the recon, mri_fill is part of the recon and operates on both hemispheres. If you wanted to combine the mris_fill outputs you could use matlab.

cheers, Bruce

On Fri, 19 Dec 2008, Siddharth Srivastava wrote:

Hi Bruce, Thanks a lot. In case mris_fill operates on one hemisphere at a time, i would expect there to be 2 filled.mgz, one per hemisphere. At what stage (and how) are they combined? Yes, i did mean mri_morphology, sorry for the typo. thanks again, sid.

On Fri, Dec 19, 2008 at 7:35 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

Hi Sid,

the mri_* command in general operate on volumes and the mris_* commands on surfaces. mri_fill uses different label for the lh and rh, and one call will fill both hemispheres, but if you mean mris_fill, then it takes any surface and fills the interior, so it would only do 1 hemi at a time (although you could of course combine them easily). As for mris_morphology, are you sure you don't mean mri_morphology? It won't take a general structuring element, sorry, just does simple open/close/erode/dilate.

cheers, Bruce

On Fri, 19 Dec 2008, Siddharth Srivastava wrote:

Hi everyone,

...

             what is the difference in functionality between the mri_*

commands and the mris_* commands? How does the mris_fill command maintain the distinction between the left and the right hemisphere? I see only one filled.mgz having 2 labels? does it write to the same file during each invocation (lh,rh), or just one call is enough to fill both hemispheres? mris_morphology: it is possible to specify the structuring element for the intended operation? best regards, sid