I tried to use itk-snap to manually align epi to T1, and obtain the transformation matrix.
align_epi_anat.py -anat2epi -anat, t1 \
-save_skullstrip -suffix _al_junk.nii.gz \
-epi epi.str, -epi_base 0 -epi_strip 3dAutomask \
-volreg off' -tshift off -anat_has_skull no -patial_coronal -pre_matrix itkxfm.1D
But it did not work. It might due to the coordinate difference between itk-snap and afni
Then I used afni Nudge plugin to manually align the epi to T1. I clicked print button and got the parameter below.
3drotate -quintic -rotate -8.78I -29.47R 5.78A -ashift -7.42S 9.39L 4.00P -prefix ??? inputdataset
Can I ask how to convert these rotation and shift numbers into a matrix file such that I can feed to -pre_matrix option in align_epi_anat.py?
Thanks.
