But is the wm.mgz 'off' (less than 5) there? If the wm.mgz is 95 or something it means we accurately segmented that voxel. If you upload we will take a look, but please include specific voxel coords
Cheers Bruce > On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke > <vandenbroucke.w...@gmail.com> wrote: > > 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 <fis...@nmr.mgh.harvard.edu>: >> 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. > > > > -- > 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
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