alignment and standardization of 4 functional slices

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?

thank you,
ns 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, 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/ 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.