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 <fischl@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.work@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 <fischl@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