Hi Ruthger,
I use the following command to take the binary lesion mask (native space) to the freesurfer space:
mri_convert -rl mri/brainmask.mgz -rt nearest lesion_mask_native_space.mgz lesion_mask_fs_space.mgz
I always overlay lesion_mask_fs_space.mgz on brainmask.mgz to check that things look correct.
Hope this helps. Mehul
On Mon, Oct 11, 2010 at 1:51 AM, Righart, Ruthger Dr. < Ruthger.Righart@med.uni-muenchen.de> wrote:
Dear Freesurfers,
I would like that surface analyses (i.e., cortical thickness) are not confounded by subcortical lesions in patients. Freesurfer provides a work-around in its release notes ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), which is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and in aseg.mgz to 77 and then run recon-all -autorecon2-cp (see copy text underneath).
As I have lesion masks of every patient I thought it would be best to automatize this step. In that case, I would like to bring mask images with white matter lesions of these patients in the same (freesurfer) space as my T1.mgz, with dimensions 256 x 256 x 256, spacing 1 x 1 x 1., and after that set the lesions to the aforementioned values.
Is there a possibility to bring lesion mask of these patients in the same space as T1.mgz in freesurfer? I inspected the function bbregister and mri_convert but could not find a solution here. Any help or suggestions are appreciated!
Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany
Ruthger.Righart@med.uni-muenchen.de
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
• mris_make_surfaces: where wm lesions exist, even if thelesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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