Hi all,
I tried to convert the ANTs-format warp (from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5) generated by fMRIPrep into FSL format (from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm_fsl.nii.gz) using c3d affine tool, so that I could use it later in pyAFQ for tractography. The conversion itself works fine, but once I add intent code to FSL xfm header(intent code 2006), the warp seems to be damaged. To be specific, the FSL warp applied to MNI template shifted to the lower-left corner and it no longer aligns with the T1w image.
I think I have to change the intent code or pyAFQ will throw en error. What should I do? Why is this happening? I’ve tried several different scripts to modify the intent code, but they all end up corrupting the image in the same way—even though fslhd shows that only the intent code was changed. I’m really confused.
I’m a new beginner of this field and it’s my first time asking questions here. I hope I’ve clarified myself.
Thanks a lot,
Qing