Thanks so much Peter ! It works very well. But I also have a few questions:

1. Instead of 3dAllineate, I also try align_epi_anat.py but it did not align it very well. Do you suggest we should generally use 3dAllineate in partial coverage alignment?

align_epi_anat.py -anat2epi \
-anat  anatSS.Subj01.nii -suffix _al_junk.nii.gz \
-epi epi1_rs.nii.gz -epi_base 0 \
-epi_strip None \
-volreg off -tshift off -anat_has_skull no

2. I am also curious about the '-pre_matrix' option in align_epi_anat.py. Is there any way that I can first nudge the data to perform a coarse manually alignment and then set it as the starting point for 3dAllineate or align_epi_anat to fine tune it?? I tried the nudge plugin but do not know how to feed the shift and rotation parameters (see below) to align_epi_anat as the starting point...

3drotate -quintic -rotate -8.78I -29.47R 5.78A -ashift -7.42S 9.39L 4.00P -prefix ??? inputdataset

Thanks.



Edited 4 time(s). Last edit at 06/21/2019 02:00PM by ruyuanzhang.