visualising group difference maps

[MaLiUHH]

Dear Mr. Schäfer,
first of all, thanks for the amazing package!
I am currently using group.morph.agg.standard.vertex to calculate group difference maps (i.e. agg.data.group1 - agg.data.group2) and display it using vis.data.on.fsaverage. I played around with RColorBrewer::brewer.pal(5, name = "RdBu")) as a diverging colour palette.

1. The colour bar doesn't seem centred around 0 = white. The scale takes slightly off to the right/positive side. Is there a way to centre it manually?
   Edit: I managed this by adding the symm argument to makecmap_option = list('colFn'=RdBu,'symm'=TRUE)

2. As you may also see, the differences are actually quite small. Do you have any recommendations on how to improve visibility? Can one for example increase the colour intervalls (small difference = stronger colour)?

3. I tried using surface = inflated, which resulted in a overlay of both hemispheres. Do you have any suggestions on how to fix that?
   

Thank you!

[dfsp-spirit]

Hi @MaLiUHH,

sorry for the rather late reply,

• Point 1: seems done already (in the way I would recommend)
• Point 2: I think there is an option somewhere to limit the data being displayed to a certain range of values. That would give better colors. It's described in the FAQ, see question Can I limit the data range, including the min and max values displayed on the color bar?.
• Point 3: there is an easy fix, see Views other than t4 garbled for inflated and vis.x.on.subject #7. In short, pass rglactions = list('shift_hemis_apart'=TRUE) as an additional parameter to vis functions to have them shift the hemispheres apart. The coordinates in the mesh files really overlap, causing this behavior.

Some more details on Point 2: This happens because you have (very few) points with higher values in your data, look at a histogram, or at the area very close to medial wall to see them.

Please let me know whether that was helpful, or if you need more help.

Best,

Tim

[dfsp-spirit]

Did you get it to work, @MaLiUHH ?

[MaLiUHH]

Dear Tim, I am sorry for the late reply. I did not yet had the chance to try your suggestions. Sorry also about the redundance for point 3, I forgot to check the closed issues. I will let you know as soon as possible.

[MaLiUHH]

Dear Tim,

• fix 3 worked like a charm.
• your hint towards 'limit_fun' worked as well, but I ended up using 'range' instead to adapt the scale for multiple images equally

resulting in the outcome as hoped for
Thanks a lot!!!

[MaLiUHH]

One more question - probably also a really simple one:
I would like to display an atlas annotation on top of my group difference maps. I managed to display fsaverage with the annot on its own (vis.subject.annot(subjects_dir , "fsaverage" , 'HCP-MMP1', views = c("si"), outline = TRUE)), but I just can't figure out how to combine both functions. I promise, I checked the FAQ and previous issues this time ;)

Also, I was unsure if I should have opened a new issue for this question. My apologies if its inconvenient.

[dfsp-spirit]

I think due to a bug, this is currently limited to displaying the atlas outine in black/white, but if that is fine for you, see #28 for a solution.

No worries about not finding stuff in the FAQ, it's rather hidden and I don't expect people to read it (I just hope it shows up in searches). It's not like I would read FAQs myself. ;)

[MaLiUHH]

hmmm ok, I've actually read this one...phew...
I was able to follow the code AndrewLawrence posted and adapted it so that morph_data_both loads my pre-calculated difference map:
vis.symmetric.data.on.subject(subjects_dir, "fsaverage", morph_data_both = aggdata_group1-group2, surface = "inflated", views = "t4", bg=aparc_outline)

But the problem is in fact, that my difference maps are whole-brain and each vertex has a value. So basically there is no annot outline left to see. So I guess my question remains. Is there a way to display the annot on top of the map instead of having it as the background.

Out of curiosity I did try just to just switch up the input:
vis.symmetric.data.on.subject(subjects_dir, "fsaverage", morph_data_lh = aparc_outline$lh, morph_data_rh = aparc_outline$rh, surface = "inflated", views = "t4", bg=aggdata_group1-group2)
receiving "error in file(fillepath, "rb") : invalid 'description' argument" + a few warnings which I interpreted by now as not supporting my map as 'bg' file format??

Best

[MaLiUHH]

Dear Tim, I just got reminded of my last issue. Would you mind taking another look?
Best