Dear Bruce,
Thank you. I transferred via ftp, the entire Freesurfer subject folder (Sub5.zip). The most pronounced "miss" segmentation is around coordinate 169 158 91, but it extends from about 168 155 85 up until 168 164 106.
Thank you very much for taking a look at it. Best, Annelinde
2015-11-23 18:59 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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
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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.