[ENH] Converter for FreeSurfer format `mgh`

PennLINC / ConFixel

Companion converter software for ModelArray for converting data back and forth from the HDF5 file format.

BSD 3-Clause "New" or "Revised" License

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Open zhao-cy opened 1 year ago

zhao-cy commented 1 year ago

Some differences from other converters:

needs to combine lh and rh data when --> hdf5; needs to separate lh and rh when --> .mgh
source filename (in column names of hdf5 file): something like lrh, instead of just lh or rh

Testing against: FreeSurfer has in-house qdec (link here) which does statistics; can compare this converter + ModelArray results versus that one.

zhao-cy commented 1 year ago

See example scripts from Steven in issue #26 Currently what he does are:

FS output (e.g., lh.thickness*.mgh and rh.thickness*.mgh) --> harmonize --> convert np.array into HDF5 for ModelArray, with lh and rh combined [in python]
ModelArray output dataframe --> directly saves as FS format with lh and rh separated [in R]

zhao-cy commented 1 year ago

Finally, probably also consider adding group-level mask and individual masks as inputs, just like those for voxel-wise data's converter ConVoxel.