[FieldTrip] graphical problem with ft_sourceplot

Marieke van de Nieuwenhuijzen m.vandenieuwenhuijzen at fcdonders.ru.nl
Mon Jul 16 19:03:57 CEST 2012

Dear all,

I am trying to use ft_sourceplot to plot modelvalues ranging from negative to positive. The blobs of interest are the ones close to both the positive and negative extremes, so I want to mask the values surrounding zero. However, I can't seem to mask these values properly.

The code I'm using is:
cfg              = [];
cfg.method       = 'slice';
cfg.funparameter = 'model';
cfg.maskparameter = cfg.funparameter
cfg.colorlim      = 'maxabs';
cfg.opacitymap    = 'vdown'
cfg.opacitylim    = 'maxabs';

Although this code masks the values around zero, it only plots the underlying MRI scan partially. It looks like only those voxels of the MRI scan that contain gridpoints which are located inside the brain according to grid_singleshell.inside are plotted in the underlying MRI. In fact, this is exactly how I would expect the functional overlay to behave (which it does), but not the underlying MRI scan.

If I set cfg.opavitymap to 'rampup' I don't get this graphical glitch, i.e. the anatomical MRI scan is plotted completely. However, as this doesn't mask the zero values, using this setting is not an option for me.

I am aware of the artefacts that can occur when using opacity. However, setting the renderer to zbuffer doesn't solve the problem at all. In fact, if I do this the anatomical scan isn't plotted at all, and the zero values are not masked. 

If I specify cfg.method as 'ortho' instead of 'slice', the resulting plot looks good (the complete anatomical MRI is plotted and the values around zero are masked), apart from some green line pieces surrounding the brain. Setting the renderer to zbuffer here does seem to get rid of those lines, but ignores the masking of the values around zero.

Does any of you perhaps know how to get rid of the glitch (if it is indeed a glitch) when using the aforementioned code?


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