[FieldTrip] failed segmentation

[Vitoria Piai]

Hi Lilla and Christiano,

Thanks a lot for the suggestions.
I think I've managed to fix it by applying Lilla's suggestion, i.e., 
instead of using the tpm default, I specified the output for 
'brain','skull','scalp'.

Cheers, Vitória

On 11/17/2013 12:03 PM, Lilla.Magyari at mpi.nl wrote:
> hi Vitoria,
>
> is this a tpm (the default output of ft_volumesegment)? Have you also
> tried to segment this mri with an output for 'brain','skull','scalp'?
> because when you have a binary representation for these tissue-types, they
> do not overlap, and are closed. So, I am wondering if you end up with a
> brainmask which do not contain the artifact at the top of the head.
>
>
> Lilla
>
>
>> 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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