Rearraging data axes when converting VTC and VMP to NIFTI

[27-apizzuti]

Hi Faruk,

I am trying to convert Brainvoyager's .VTC and .VMP outputs in NIFTI using your read_vtc_export_nifti.py and read_vtc_export_nifti.py scripts from the example folder. Unfortunately, the exported NIFTIs don't overlap when opened in an external software.

My current solution for the VTC:

header, data = bvbabel.vtc.read_vtc(FILE, rearrange_data_axes=False)
new_data = np.transpose(data, (0, 2, 1, 3))
new_data = new_data[::-1, ::-1, ::-1, :]

Alessandra

[ofgulban]

Thanks for the issue @27-apizzuti ,

I have incorporated these changes to read_vtc_export_nifti.py example with 5d176a7.

I need to test rearrange_data_axes=True option with different vtc inputs to make sure the data aligns with nibabel's RAS+ output.

[ofgulban]

@jorievanharen maybe have a look at this change and see if the latest bvbabel effects your previous VTC conversions. Right now the safest route is to use rearrange_data_axes=False option and doing your own axes transpose and flipping if needed.

It will take some time to converge a general solution for rearrange_data_axes=True option. As I am seeing conflicting information and input/output relations in the documentations and example vtc files.

[ofgulban]

TODO: I need to implement rearrange_axes flag for VMP and GLM read write functions (in addition to VTC).