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 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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