I used “align_epi_anat.py” for alignment in my preprocessing script.
I understand it is normal to calculate the transformation from one selected functional image to the anatomical image…and
then use the transformation to alignment all the other functional images across 4 runs.
However, I think I did this alignment process for individual runs.
In other words, I used align_epi_anat.py separately for each of 4 runs.
That means I used a different reference functional image from each run to align functional images to anatomical data set.
There is ONLY ONE anatomical data set for 4 runs…so I guess this is wrong, right?