glad to hear it's not all your subjects!
Good luck
Bruce
On Wed, 2 Dec 2015, Annelinde
Vandenbroucke wrote:
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 no
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-
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).
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...
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-
P.s. You should use our filedrop which you can find on our website
> On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke
> 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
But is the wm.mgz 'off' (less than 5) there? If the wm.mgz is 95 or something
it means we accurately segmented that voxel. If you upload we will take a look,
but please include specific voxel coords
Cheers
Bruce
> On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke
> wrote:
>
> Hi Bruce,
>
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 y
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 a
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 th
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