I work with Zeynab and we were exploring a quick workaround to look at the data in native space by inverting the transformations.
However, I am having trouble getting antsApplyTransforms to take the affine matrix created by bbregister. I can get the *preproc.nii.gz bold image in MNI space registered to T1 space using the .h5 file. But antsApplyTransforms doesn’t like any of the affine .txt files. I’ve tried using the affine.txt file located in the /fsl2itk/ folder in workflows and the *T1_affine.txt file (inverting it) located in the /anat/ output folder.
Obviously it’s much simpler to just be able to have the native space be the output, but I’m curious as to why the transformations aren’t working.