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NeuroanatomyAndConnectivity / gradient_analysis

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where are .surf files from? #8

Closed JohnGriffiths closed 7 years ago

JohnGriffiths commented 7 years ago

Notebook '03_visualize_embeddings.ipynb' uses a file called gradient_data/templates/S900.L.midthickness_MSMAll.32k_fs_LR.surf

Where does this file come from?

Closest I know of is from a folder called HCP_S900_GroupAvg_v1.zip that I obtained from a slightly random internet location, which contains file S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii

Seems that mapping between freesurfer and HCP surface spaces is a little more involved than one might like.

Do you have the commands used for this somewhere here?

Ta.

margulies commented 7 years ago

Those were created as a work around to enable importing of the surface geometry a while back. They were converted by using wb_command to convert the gifti format to ascii and then mris_convert to output the freesurfer format. I've uploaded the files to the directory. There's certainly a better way to read the .gii directly using nibabel now, but in the meantime, the .surf files are available...