you can also use mri_binarize which has a --dilate option. I think it dilates if it has one or more faces in common. You might also look into fslmaths (you can easily convert from mgz to nifti) if that's an issue
On 8/16/10 8:46 PM, Bruce Fischl wrote:
Hi Jeff,
you are welcome to our source code which has region-growing algorithms in the volume (e.g. for control point detection) and on the surface.
cheers Bruce
On Mon, 16 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Bruce,
Yes, you are likely correct, but my boss wants to do it this way. Besides, I am going to have other uses for region growing that you might find scientifically acceptable. But the question still stands - does Freesurfer give me access to such a basic tool, or will I have to write my own with Matlab/IDL/C etc.?
Thanks, -Jeff
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, August 11, 2010 2:00 PM To: Eriksen, Jeffrey (Portland) Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 18
Hi Jeff,
we autoamtically segment the cc from an anatomical, which would probably
be a more accurate measure.
cheers Bruce On Tue, 10 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Sure. Right now I would like to extract the corpus callosum, as
defined
by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like
to
pick a voxel in the center of the CC and grow a region around it
picking
up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted
single
irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like
EMSE
and Brain Voyager.
Thanks, -Jeff
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