Hi Daniel,

I also have one question regarding alignment across two sessions.

Firstly, I aligned all epi datasets to each session's own anatomical (E1->A1, E2->A2). Secondly, I used align_epi_anat.py to align the A2 from the second session to the A1 from the first session (A2->A1), and then computed their transformation matrix. Lastly, I used 3dAllineate and the transformation matrix to align E2 to A1. However, there is an warning related to 3dAllineate.

My script and Warning Message with 3dAllineate:

set anat1 = 'anat1_final.xtexp+orig'
set anat2 = 'anat2_final.xtexp+orig'

set epi2 = 'pb02.xtexp.r01.volreg+orig'
set epi2_children = `ls pb02.xtexp.r02.volreg+orig.HEAD \
pb02.xtexp.r03.volreg+orig.HEAD \
pb01.xtloc.r01.volreg+orig.HEAD \
pb02.xtexp.r04.volreg+orig.HEAD \
pb02.xtexp.r05.volreg+orig.HEAD \
pb02.xtexp.r06.volreg+orig.HEAD`

# # # align the two anatomical datasets (pre / post) and compute transformation matrix
align_epi_anat.py -anat anat2_final.xtexp+orig \
-epi anat1_final.xtexp+orig \
-epi_base 0 -prep_off \
-anat_has_skull no \
-epi_strip None \
-giant_move -cost lpa \
-overwrite -suffix _al

# # # align epi2 to anat1
3dAllineate -base anat1_final.xtexp+orig -input pb02.xtexp.r01.volreg+orig \
-1Dmatrix_apply anat2_final.xtexp_al_mat.aff12.1D -mast_dxyz 3 \
-prefix pb02.xtexp.r07.volreg

3dAllineate -base anat1_final.xtexp+orig -input pb02.xtexp.r02.volreg+orig \
-1Dmatrix_apply anat2_final.xtexp_al_mat.aff12.1D -mast_dxyz 3 \
-prefix pb02.xtexp.r08.volreg

3dAllineate -base anat1_final.xtexp+orig -input pb02.xtexp.r03.volreg+orig \
-1Dmatrix_apply anat2_final.xtexp_al_mat.aff12.1D -mast_dxyz 3 \
-prefix pb02.xtexp.r09.volreg

3dAllineate -base anat1_final.xtexp+orig -input pb01.xtloc.r01.volreg+orig \
-1Dmatrix_apply anat2_final.xtexp_al_mat.aff12.1D -mast_dxyz 3 \
-prefix pb01.xtloc.r03.volreg

3dAllineate -base anat1_final.xtexp+orig -input pb02.xtexp.r04.volreg+orig \
-1Dmatrix_apply anat2_final.xtexp_al_mat.aff12.1D -mast_dxyz 3 \
-prefix pb02.xtexp.r10.volreg

3dAllineate -base anat1_final.xtexp+orig -input pb02.xtexp.r05.volreg+orig \
-1Dmatrix_apply anat2_final.xtexp_al_mat.aff12.1D -mast_dxyz 3 \
-prefix pb02.xtexp.r11.volreg

3dAllineate -base anat1_final.xtexp+orig -input pb02.xtexp.r06.volreg+orig \
-1Dmatrix_apply anat2_final.xtexp_al_mat.aff12.1D -mast_dxyz 3 \
-prefix pb02.xtexp.r12.volreg

*+ WARNING: Re-using final row of -1D*_apply 'anat2_final.xtexp_al_mat.aff12.1D' for sub-brick #1
*+ WARNING: Re-using final row of -1D*_apply 'anat2_final.xtexp_al_mat.aff12.1D' for sub-brick #2
...
*+ WARNING: Re-using final row of -1D*_apply 'anat2_final.xtexp_al_mat.aff12.1D' for sub-brick #295

Thank you very much in advance！


-Xin