Hi,

I am using align_epi_anat.py to align the anatomical image (anat) to the EPI images (func) as a intermediate step of warping the func data to the standard space. I noticed that the different orientations of the input func data to align_epi_anat.py would make different outputs, i.e. different aligned anat image and different transform matrices. I did some search online about why that would happen, but I didn't find any similar issues posted before. Please let me know if I missed something.

Here is the more detailed description of the issue. After dicom reconstruction, the orientation of my func data is RAI, and the orientation of my anat data is LPI. Let [func] be the name of my func data and [anat] be the name of my anat data, I used the following command to align the anat to the func:

align_epi_anat.py -anat [anat] -epi [func] -epi_base 0 -anat2epi -suffix _al -anat_has_skull no -volreg off -tshift off -Allineate_opts -warp shift_rotate -cost lpc+ZZ

The output transform matrix (with the suffix *aff12.1D) I got is the following:
# 3dAllineate matrices (DICOM-to-DICOM, row-by-row):
0.999877 -0.00685082 -0.0141272 -0.834526 0.00702079 0.999903 0.0120176 0.136856 0.0140435 -0.0121153 0.999828 -0.433617

Then, I re-orient the fun data by using the command 3dresample:
3dresample -oriet LPI -prefix [func_rs] -input [func]
I aligned the anat to the re-oriented func using the same command:

align_epi_anat.py -anat [anat] -epi [func_rs] -epi_base 0 -anat2epi -suffix _al -anat_has_skull no -volreg off -tshift off -Allineate_opts -warp shift_rotate -cost lpc+ZZ

The output transform matrix (with the suffix *aff12.1D) I got is the following:
# 3dAllineate matrices (DICOM-to-DICOM, row-by-row):
0.999988 -0.0030592 -0.00391642 -1.38792 0.00307867 0.999983 0.00497563 0.400688 0.00390113 -0.00498763 0.99998 -0.494812

I have two questions here:
1. Why changing the orientation of the func data would affect the output of the alignment?
2. Dose it mean we need to make the func data and the anat data have the same orientation before doing the alignment?

Thanks in advance.

Sincerely,
Yixiang