Bruce,
Please ignore my earlier email. Let me explain what I exactly need. The wmparc.mgz gives me WM parcellation based on cortical parcellation. What I need is just the boundary voxels from wmparc.mgz, such that each voxel in my output has a neighbor in GM and other WM voxels are set to 0. If there is already something available, that would be great. Otherwise I was thinking of proceeding in the following manner,
Input: WMparc.mgz, WM mask, GM mask. Check if each voxel in WMparc.mgz is inside WM mask. If yes, check if the voxel has atleast one neighbor in GM. If yes, set this voxel as output. else, Output is 0.
I hope it makes sense,
Madhura
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 12/15/2010 11:05 AM To: Ingalhalikar, Madhura Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WM parcelleted boundary
Hi Madhura,
I'm not sure I understand. The ?h.white is the boundary. If you want to create a voxel representation of it you can use mris_fill
cheers Bruce On Wed, 15 Dec 2010, Ingalhalikar, Madhura wrote:
Bruce and Allison, Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct solution. I just need the labeled WM boundary (ribbon) to seed my fiber tracking. So basically I will have to compute the boundary from wmparc.mgz. Is there anything that does that already? Thanks, Madhura
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 12/10/2010 8:13 PM To: Ingalhalikar, Madhura Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM parcelleted boundary
Hi Madhura,
have you looked at the wmparc.mgz? It might be exactly what you want
Bruce
On Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:
Hi,
Is there a way to get the cortical parcellations projected onto the WM boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber tracking. Please let me know,
Thank you, Madhura
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