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danjgale / surfplot

A package for publication-ready brain surface figures
https://surfplot.readthedocs.io/en/latest/
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mismatch between Surfplot and Freeview #30

Open pinilorenzo opened 6 months ago

pinilorenzo commented 6 months ago

I have a .mgh file representing a in fsaverage space. I am attempting to visualize it on Surfplot:

from surfplot import Plot from neuromaps.datasets import fetch_fsaverage import nibabel as nib

left = nib.load('/lh.glmdir/FSGD_acute_vs_controls/cache.th40.pos.sig.cluster.lh.mgh')
right = nib.load('/rh.glmdir/FSGD_acute_vs_controls/cache.th40.pos.sig.cluster.rh.mgh')
fsagg=np.concatenate([left.get_fdata().flatten(),right.get_fdata().flatten()])

surfaces = fetch_fsaverage(density='164k') lh, rh = surfaces['inflated'] p = Plot(lh,rh, views=['medial', 'lateral'], flip=False, zoom=1.2) p.add_layer(fslr_agg, zero_transparent=True, as_outline=False, cbar=True, cmap='Reds') p.build()

The process runs successfully. However, upon comparing this result with the fsaverage inflated in freeview, significant differences emerge. The mapping appears in entirely different regions. What might be incorrect in the above code?

Thanks, L

danjgale commented 6 months ago

Hi @pinilorenzo thank you for bringing this to my attention. Is it possible to share the files or screenshots of the differences? Or if not, are you able to recreate this issue with some mock data? I will look into this and try and recreate it locally

What version of surfplot and matplotlib are you running?

Thanks for your patience