Converting subject to MNI space using pycortex


I am a research student doing machine learning with brain data so I am fairly new to the domain of neuroscience. I am trying to use pycortex to transform a subject to MNI space so I can average across different subjects.

The fMRI data I am using were gathered as part of a different research and the preprocessed data are in the form .npy files which are numpy arrays. From doing the demo with pycortex just to get started I have seen that pycortex is using niftii files in its database.

I tried to convert the .npy files using nibabel in order to use them as niftii files in pycortex. I also understand that in order to transform to MNI space you need a transformation matrix. In the data, I have a 4x4 matrix which I am assuming it is the transformation matrix.

However even when converting to niftii files and using that transformation matrix I still can’t get pycortex to work. I am placing the niftii file under /subject_name/tranforms/fullhead/ and I am using the same code as the demo provided in the pycortex documentation (Transform from Subject to MNI Space — pycortex 0.1 documentation).

I would be very grateful if you can help me.