Dear Bruce, Thank you very much for letting me know. Indeed, something went wrong with the slice prescription of that acquisition. I didn't know that would affect segmentation. Our normal acquisition includes the whole brain.
Thanks again for to you and your support team! Cheers, Annelinde 2015-12-02 7:12 GMT-08:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Annelinde > > the problem is that your original image only includes about half the > cerebellum. We expect a full cerebellum and so the segmentation labels some > of the cortex that is superior to cerebellum incorrectly as cerebellu, then > removes it from the wm.mgz (since it isn't cerebral cortex). You need to > change your acquisitions to include the full cerebellum > > cheers > Bruce > > > > On Mon, 30 Nov 2015, Annelinde Vandenbroucke wrote: > > Dear Bruce, >> >> I was wondering whether you received my transfer well. If you sent me an >> email back already, my apologies. I accidentally >> switched of email service from the support list for a day. >> >> Thank you in advance, >> Annelinde >> >> 2015-11-24 10:29 GMT-08:00 Annelinde Vandenbroucke < >> vandenbroucke.w...@gmail.com>: >> 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 >> >> >> >> >> -- >> 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
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