P.s. You should use our filedrop which you can find on our website
On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke vandenbroucke.work@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 fischl@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
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-- 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