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 <fischl@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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