---------- Forwarded message ---------- From: Daniel H Choi dhchoi@u.northwestern.edu Date: Fri, Aug 8, 2008 at 11:10 AM Subject: Re: [Freesurfer] editing masks To: Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi all,

I was wondering how to edit the voxels of a mask (the name of which is "lh.stg.mask.mgz") so that each voxel would be a value of 1 (if I try adding voxels in tkmedit, their values are 255). Additionally, we use this mask to isolate STG. But instead of a simple binary mask, this mask keeps the white matter values within STG intact (and anything outside is 0). Would adding voxels to the mask in tkmedit change this function? Thanks

Dan

On Tue, Aug 5, 2008 at 7:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

I see. You should be able to manually edit it in tkmedit, or you can try using mri_morphology to close small holes.

cheers, Bruce

On Tue, 5 Aug 2008, Daniel H Choi wrote:

The mask was obtained from a friend, who had actually inquired earlier to

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freesurfer about using a binary mask to extract everything except the roi. (He wanted to include white matter in the roi, while everything outside remained a value of 0). The mask is in an .mgz format and we apply mri_mask to the individual brainmask.mgz. Upon using this mask, we noticed that there were some voxels missing in the mask itself (it was not an entirely smooth surface). This might be attributing to some problems we are having later on. Thanks

Dan

On Tue, Aug 5, 2008 at 5:47 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu

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wrote:

Sorry, I don't understand. Where did you get the mask? Or are you trying

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to create it from scratch?

On Tue, 5 Aug 2008, Daniel H Choi wrote:

Hi,

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I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I was wondering though how I might go about editing the mask? I see that there are random voxels that have been left out and I would like to fill those in. Thanks

Dan