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
>
>
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Annelinde R. E. Vandenbroucke, PhD
University of California, Berkeley || Helen Wills Neuroscience Institute
10 Giannini Hall
Berkeley, CA 94720
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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.
--
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
_______________________________________________
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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
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