Hi AFNI gurus,
I was trying multi-echo fMRI analysis in the native space (so no "tlrc") without anatomy data (so no "align"). In this case, the "volreg" step is as simple as (i) estimating head motions with 3dvolreg on the "$fave_echo", and (ii) apply the transformation matrix to other echoes with 3dAllineate.
In the help doc of 3dvolreg, it says that the transformation matrix needs to be inversed like "cat_matvec fred.aff12.1D -I". However, while implementing it with afni_proc.py, I don't see "cat_matvec -I" but "cat_matvec -ONELINE" instead; and 3dAllineate directly uses this "oneline" version of the transformation matrix.
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig \
-1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run.e$fave_echo \
-cubic \
-1Dmatrix_save mat.r$run.vr.aff12.1D \
pb01.$subj.r$run.e$fave_echo.tshift+orig
cat_matvec -ONELINE \
mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D
foreach eind ( $echo_list )
3dAllineate \
-input pb01.$subj.r$run.e$eind.tshift+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-prefix pb02.$subj.r$run.e$eind.volreg
end
So my question here is whether the option of "-I" equals the option of "-ONELINE" in this particular case? While executing the 3dAllineate, it outputs a lot of warnings of "volume 0..1*+ WARNING: Re-using final row of -1D*_apply" for each of the TR volumes. Should I care about these warnings?
