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.righ...@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.righ...@med.uni-muenchen.de > > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > > • mris_make_surfaces: where wm lesions exist, even if the > lesion 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 > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
