External Email - Use Caution
Hello!
As suggested by the latest comment on this freesurfer github issue ( [ https://secure-web.cisco.com/1M0TqndURr2omFNMTTDpuWOzO_Vs7lJWAVS6xceXr6HXZ7q... | https://secure-web.cisco.com/1M0TqndURr2omFNMTTDpuWOzO_Vs7lJWAVS6xceXr6HXZ7q... ] ), I'm reaching out to you via email.
In case that's useful, I'll copy the initial issue here:
Problem As detailed in issue #3415 opened in nilearn, vertex order does not match across all fsaverage resolutions.
I downloaded fsaverage 3 to 7 tarballs for the git annex of this repo and simply ran the following script to show that vertex order is not preserved across resolutions:
# %% from nilearn import surface
# %% fs3_path = "/home/alexis/singbrain/data/freesurfer_fsaverage/fsaverage3/surf/lh.pial" fs5_path = "/home/alexis/singbrain/data/freesurfer_fsaverage/fsaverage5/surf/lh.pial" fs7_path = "/home/alexis/singbrain/data/freesurfer_fsaverage/fsaverage7/surf/lh.pial" fs3_coordinates, fs3_faces = surface.load_surf_mesh(fs3_path) fs5_coordinates, fs5_faces = surface.load_surf_mesh(fs5_path) fs7_coordinates, fs7_faces = surface.load_surf_mesh(fs7_path)
# %% print(fs3_coordinates[:5]) print(fs5_coordinates[:5]) print(fs7_coordinates[:5]) Output:
[[-3.87359581e+01 -1.93433647e+01 6.72201385e+01] [-9.71759605e+00 -9.23328686e+00 4.65803757e+01] [-2.40194092e+01 4.31147995e+01 2.39262428e+01] [-5.98615112e+01 4.93119545e-02 8.97464848e+00] [-5.06454735e+01 -4.94050064e+01 4.78137321e+01]]
[[-3.87359581e+01 -1.93433647e+01 6.72201385e+01] [-1.66624870e+01 -6.90612259e+01 6.12812729e+01] [-9.71761799e+00 -9.23326397e+00 4.65803413e+01] [-2.40194283e+01 4.31148720e+01 2.39262142e+01] [-5.98614998e+01 4.92927618e-02 8.97456360e+00]]
[[-3.87359581e+01 -1.93433647e+01 6.72201385e+01] [-1.66624680e+01 -6.90612564e+01 6.12812119e+01] [-9.71762943e+00 -9.23325062e+00 4.65803223e+01] [-2.40194435e+01 4.31149139e+01 2.39261990e+01] [-5.98614883e+01 4.92815673e-02 8.97451496e+00]] Here, we see that the second vertex of fsaverage3 doesn't match that of fsaverage 5 and 7. I did some more extensive testing and it seems to me that:
fsaverage 5, 6, 7 have consistent vertex order fsaverage 3 and 4's vertex order is different from 5, 6, 7 but can be reworked to be consistent, using a procedure I detailed in nilearn issue #3415 ( [ https://secure-web.cisco.com/1MUOQFQrlxwxUt85m4623j9t2ExzEpzjIm1YZnc6mKLXndc... | https://secure-web.cisco.com/1MUOQFQrlxwxUt85m4623j9t2ExzEpzjIm1YZnc6mKLXndc... ] )
Suggestion Maybe we should reorder fsaverage 3 and 4's vertices for all maps, what so you think? Thank you for the great software anyways! ☺️
Warm regards, Alexis