i tried to transform the qsiprep dwi output from ACPC to T1 space with the following command:
antsApplyTransforms -d 3 -e 3 \
-i dwi/sub-00300_space-ACPC_desc-preproc_dwi.nii.gz \
-r dwi/sub-00300_space-ACPC_desc-preproc_dwi.nii.gz \
-t anat/sub-00300_from-ACPC_to-anat_mode-image_xfm.mat -o transformed.nii.gz
when i overlay transformed.nii.gz on top of the original T1w image (e.g., sub-0300_T1w.nii.gz), they dont seem to align well
am i doing it wrong?