Hi all,
I am very new to AFNI and have a question regarding deobliquing so that I can properly align my data. A bit of background: I wish to align a T1 anatomical with a high-resolution T2 anatomical, and then also align my functionals to the T2. Right now, the align_epi_anat.py throws the error that my datasets are obliqued.
So, I used the 3dWarp_deoblique and re-ran the align_epi_anat.py and it seemed to work properly and it all looks aligned.
My question is regarding the +tlrc suffix that is now added onto my filename. Does deobliquing my anatomicals situate them in Talaraich space, and that is the resulting +tlrc? I do not want to put any of my anatomical or functional data into common space yet because I will be manually tracing structure in native space and later using another program to form a normalized template (ANTs).
So 1) does using 3dWarp_deoblique and align_epi_anat.py put everything in Talaraich space? and 2) if so, how can I go about aligning my data and maintaining native space?
Thanks in advance,
Rachel
