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 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
>
>
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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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whom it is
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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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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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