Hi, afni experts
I am using align_epi_anat.py to align some epi and anat data. I used -anat2epi option. After I obtained the transformation file, I warped anat to epi, and also epi to anat. The epi2anat data seems sane, indicating a good alignment. But the anat2epi file looks weird. One issue is that, my epi and anat data were collected in different sessions, and thus they are apart.

I did something as below

# do the alignment
!align_epi_anat.py -anat2epi \
-anat anat.nii.gz \
-anat_has_skull no \
-suffix _anat2epi.nii.gz \
-epi epi.nii.gz -epi_base 0 \
-epi_strip 3dAutomask \
-volreg off -tshift off -overwrite -giant_move -rigid_body\

# convert the xfm
!cat_matvec -ONELINE anat_anat2epi.nii.gz_mat.aff12.1D -I > epi2anat.aff12.1D

# warp epi 2 anat
!3dAllineate -base anat.nii.gz \
-input epi.nii.gz \
-1Dmatrix_apply epi2anat.aff12.1D \
-mast_dxyz 2 -overwrite \
-prefix epi2anat.nii.gz

# warp anat 2 epi
!3dAllineate -base epi.nii.gz \
-input anat.nii \
-1Dmatrix_apply anat_anat2epi.nii.gz_mat.aff12.1D \
-master epi.nii.gz -overwrite \
-prefix anat2epi.nii.gz



Edited 2 time(s). Last edit at 04/30/2019 10:47PM by ruyuanzhang.