Hi Bruce, Thank you very much for your quick response. Yes I mean that wm.mgz underestimates true white matter. Values are between 95 and 108 where it should be 110 or above. I will upload my subj dir tomorrow. Is there specific place I can upload to or shall attach it in I reply to you?
Thank you, Annelinde 2015-11-23 17:54 GMT-08:00 Bruce Fischl <[email protected]>: > 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 > [email protected] > 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. > > -- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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