probably the best thing to do is to fill the lesion with the average of
the values on the border. That will create a minimal amount of new
gradients in the image
cheers
Bruce
On Tue, 23 Oct 2012, Julio Alberto González Torre
wrote:
Hi Bruce.
I know I can set the value 110 to the voxels corresponding to white matter
lesions, using the FreeSurfer environment.
The issue is that I have binary masks for each subject. These masks are
binary files that match each subject in native space. Thus, for each
subject, this mask contains the information about the original volume voxels
which correspond to damage, and which voxels correspond to normal tissue (1
and 0 respectively).
The idea is to use this information to "paint" the voxels of each subject
corresponding to injury, establishing a mean value of white matter,
considering this value as "normal white matter." This procedure would be
done automatically with the software of SPM8 IMcalc.
The end result would be a T1 lesions volumes filled with "normal" values,
ready to be introduced into the FreeSurfer software without having to paint
each subject lesions manually.
My question is: Is this procedure correct?, Could I perform this procedure
as I have described? Otherwise, how could perform it correctly? Or is it
only possible to perform this procedure using FreeSurfer environment
manually?
Thanks.
2012/10/22 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Hi Julio
if they are white matter lesions you should be able to set those
voxels to 110 in the brain.mgz, brain.finalsurfs.mgz and wm.mgz
and rerun autorecon2-wm and autorecon3.
cheers
Bruce
On Mon, 22 Oct 2012, Julio Alberto González Torre wrote:
Hi.
My question is about dealing with multiple sclerosis
lesions in white
matter.
I have previously worked with this sample in SPM8,
and I have a binary mask
for each subject with the white matter lesions
marked.
Instead of painting manually each lesion with the
freesurfer interface,
could I provide to the freesurfer the T1 images with
the lesions painted
with another program? (exactly, with the IMcalc of
SPM, to set lesion values
of each T1 image to a standard WM value according to
the binary mask). Is
this procedure correct? What value should I provide
to this lesions?
Thanks.
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