[FieldTrip] Sourcemodel inside definition too large when using warpmni

"Jens Klinzing, Universität Tübingen" jens.klinzing at uni-tuebingen.de
Tue Mar 7 23:36:04 CET 2017

Dear Fieldtrip community,
when calling ft_prepare_sourcemodel to create an individual sourcemodel 
I get quite different 'inside' definitions for the same subject when
a) providing an unsegmented MRI and warping to the template MNI (see 
attachment: green)
b) when providing an already segmented MRI (see attachment: blue)

In fact, the extent of the inside in scenario a) is pretty similar to 
when I create a sourcemodel based on the skull instead of the brain. So 
maybe the segmentation during the warping process is the problem (for 
warped sourcemodels the inside field is just copied from the template 

Is there a way to influence the segmentation performed by 
ft_prepare_sourcemodel when warping to the template MNI?
Fieldtrip does not allow to provide an already segmented MRI in this 
case (error: missing anatomy). I expected the options cfg.threshold and 
cfg.smooth to be analogous to the threshold and smooth options for 
ft_volumesegment but they seem to be used only when I already provide a 
segmented MRI (so they can't help me here).

I could just use the cfg.inwardshift option to fix the issue but I'm 
afraid that the MNI-warping itself may be affected in case the problem 
actually results from a flawed segmentation.

Thanks in advance for your help!

All the best,
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