I have 4 axial slices of functional data (5mm x 2.5 x 2.5) that I would like to align to the structural t1 and then tlrc to a standard space (to have ROI references from the atlas that I currently use, TT_N27).
Is there a pipeline to deal with these type of data? any recommendation on how to procede?
align_epi_anat.py has some options for partial data that will try to avoid moving data out of plane, but that’s still a difficult proposition with only four slices. It would be better to have a full coverage EPI dataset that is in alignment with the partial dataset and move the two together with the same affine transformation. In that case, the partial dataset would be a “child” dataset. In align_epi_anat.py, that would be implemented with the “-child_epi” option.
thank you, I’ll try this option to align the child dataset then
If you continue to struggle, you may need to try doing some hand alignment first before allowing 3dAllineate/align_epi_anat.py to work their magic. I’ve written up some instructions here. It closely follows the methods we used to perform with ANTs, just with AFNI tools.