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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