Hi Annelinde when you say a fault wm map, do you mean that the wm.mgz underestimates the true white matter (that is, there are many voxels that are 0 in the wm.mgz that are in the white matter)? What is the intensity of the brain.mgz at those voxels?
If you tar, gzip and upload a subject dir and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look. cheers Bruce On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote: > Dear all, > > I have a faulty wm map (brainmask.mgz) where some regions are not labeled as > white matter where they should. I tried to correct both the wm.mgz map and > add control points (and saved these), afterwards running either > -autorecon2-wm or autorecon2-cp, but neither of these work. I can see the > control points and wm edits in my maps, but the wm segmentation is still the > same. I have not found a solution on the mailing list yet and was wondering > whether anybody had a similar problem or could help. > > Thank you in advance, > Annelinde > > -- > Annelinde R. E. Vandenbroucke, PhD > University of California, Berkeley || Helen Wills Neuroscience Institute > 10 Giannini Hall > Berkeley, CA 94720 > > _______________________________________________ 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.
