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 <fis...@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.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 > > > _______________________________________________ > 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
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