[FieldTrip] Sourcemodel inside definition too large when using warpmni

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Wed Mar 8 08:27:30 CET 2017

Hi Jens,

What does the ‘green’ point cloud look like relative to the blue points when you switch off the non-linear step in recipe a)?


> On 07 Mar 2017, at 23:36, Jens Klinzing, Universität Tübingen <jens.klinzing at uni-tuebingen.de> wrote:
> 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 sourcemodel).
> 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,
> Jens
> <sourcemodel green_warpmni blue_nowarp_onsegmentedmri.PNG>_______________________________________________
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