ah ok, I didn't know align_epi_anat.py already concatenates the matrices automatically.
I adjusted the code below, sot that the Allineate calculcation is only done on the sub-brick #0 of the source. Since I already use volreg for motion correction, I think it would be a bit double-stitched (and extremely slow) to run allineate also on every repetition.
3dTcat -prefix first_only_$subj pb00.$subj.r$run.tcat+orig'[0]'
align_epi_anat.py -dset2to1 -dset1 ../TEMPLATE+orig -dset2 first_only_$subj+orig \
-child_dset2 pb00.$subj.r$run.tcat+orig \
-big_move \
-volreg on -volreg_method 3dvolreg \
-volreg_opts '-Fourier -zpad 1' \
-AddEdge -dset1_strip None -dset2_strip None \
-Allineate_opts '-twofirst -twoblur 0.8 -source_automask+1' \
-tshift on -tshift_opts -tzero 0 -quintic \
-AddEdge \
-dset2_base 0 \
-volreg_base 0 \
-cost lpa
...still checking the results
Edited 5 time(s). Last edit at 08/08/2013 05:23AM by paranoidandroid.
