Views other than t4 garbled for inflated and vis.x.on.subject about fsbrain HOT 5 CLOSED

Sure! This is fixed for all views in the develop branch now, including the 'si' view. Hemisphere shifting is implemented as an rglaction and needs to be activated if you want it. If you checkout the development branch, you can try:

vis.subject.morph.native(sjd, sj, 'thickness', rglactions = list('shift_hemis_apart'=TRUE), surface='inflated', views='si')

or if you want a larger distance:

vis.subject.morph.native(sjd, sj, 'thickness', rglactions = list('shift_hemis_apart'=list('min_dist'=20)), surface='inflated', views='si')

Btw, to plot only one hemi using vis.data.on.subject, pass NULL for the data of the hemi you do not want:

vis.data.on.subject(sjd, sj, subject.morph.native(sjd, sj, 'thickness', 'lh'), NULL, views='t9')
vis.region.values.on.subject(sjd, sj, 'aparc', list('cuneus'=0.9, 'bankssts'=0.7), NULL)

What do you mean that one can only display one hemi at a time in Freeview? You can load several surfaces there as well.

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@utooley This feature is available in v0.3.0, which is now on CRAN. Details are explained in the fsbrain FAQ.

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Hi Ursula,

thanks for reporting this. I also noticed this, but did not pay much attention because I assumed it was not a bug, but a consequence of the inflation that leads to overlapping surfaces. (This does not happen in t4 view because in that view, only one of the 2 hemispheres is rendered at a time.) Now that you mention this, it occurs to me that it may very well be a bug. I will investigate and let you know.

Even if the surface coordinates in the mesh file are overlapping (as in the fsbrain visualization), one could of course introduce a feature that would allow the user to specify an amount by which to shift them apart. But let me first have a look.

Glad to hear you like fsbrain. :)

Btw, from that colorbar you have in the plot it looks like you have an old fsbrain version and could update your installation to get a better one.

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The coordinates are definitely overlapping in the source files, strange. I have done a quick hack that pushes them apart manually by the amount they overlap:

It will need some more testing to ensure this does not break other things. Most likely I will add an option to shift the hemis and let the user decide whether or not he/she wants to do this. The feature will be available in the next release.

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Wow--thanks so much for investigating so quickly and figuring out a way to implement a fix! I also thought it was likely expected behavior given that Freesurfer only allows you to view one hemi in Freeview at a time, but is very troublesome in my workflow, as I could not even figure out a hacky way to get different angles with screenshots and views="si"(since si doesn't work either with inflated since it tries to display both hemispheres).

I would have been happy to plot each hemi separately in these functions and simply pull the images together outside fsbrain afterwards, but there did not seem to be a way to plot only one hemisphere in either vis.data.on.subject or vis.region.values.on.subject.

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