[FieldTrip] failed segmentation

[Cristiano Micheli]

Hi Vitoria,
it looks like there is an artifact on the top of the head. It happened to
me already and I had to preprocess the mri volume by using an appropriate
cutoff and by thresholding (after plotting the histogram of the grey
levels).

mri.anatomy = (mri.anatomy>thr).*mri.anatomy;

or

mri.anatomy(:,:,230:256) = 0;

If thresholding is still not effective you might consider applying
morphological operators (erode, dilate, open, close), after taking care
that you voxel dimensions are cubic (diagonal values of the canonic form of
mri.transform(1:3,1:3) are all the same). I use ft_volumereslice for that.

I hope this helps,
Cristiano



On Sat, Nov 16, 2013 at 9:31 AM, Vitoria Piai <v.piai.research at gmail.com>wrote:

> Hi all,
>
> has anyone ever had a failed segmentation that looks like the one in the
> figure?
> My script works for all participants, I mean, for all other participants
> the brain is only inside the skull :)
> But it fails terribly for this one. I thought it could have to do with the
> placement of the fiducials, and I've played around a bit with that but it
> didn't solve the problem.
> If anyone recognises this type of error, I'd be help to hear if/how it can
> be fixed.
>
> Thanks a lot, Vitória
>
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