Hi Jason, Tim,
yes this a problem I also ran into, solved it accessing the data in python
with memmap specifying C order (instead of Fortran order as used in Nifti1
and nibabel nifti2 implementation)
using:
nii = nb.load(ts_file) # just to get header infos
tss = np.memmap(nii.get_filename(),
You may be running into an unfortunate design problem in CIFTI-1, if
NiBabel expects them to be standard NIfTI-2 - the dimensions are backwards
in the header, so non-square matrices will have their elements rearranged.
You may be able to get matlab to fix them via a reshape with the dimensions
swap
