Hello,

I am modifying MACAQUE_DEMO_REST to work with my data. Experimenting with EPI-anat alignment, I found that EPI stripping with 3dAutomask fails with my data but stripping with 3dSkullStrip works fine.

So in my modified script I start afni_proc.py with the following options:

set cost_a2e = "lpa+ZZ"

[...]

afni_proc.py                                                              \
            -subj_id                 ${subj}                                      \
            -script                  ${odir_ap}/proc.$subj.${state} -scr_overwrite         \
            -out_dir                 ${odir_ap}/${subj}.${state}.results                   \
            -blocks tshift align tlrc volreg mask scale regress                   \
            -dsets                   ${subj_epi}                                  \
            -copy_anat               "${dset_subj_anat}"                          \
            -anat_has_skull          no                                           \
            -anat_uniform_method     none                                         \
            -radial_correlate_blocks tcat volreg                                  \
            -radial_correlate_opts   -sphere_rad 14                               \
            -tcat_remove_first_trs   2                                            \
            -volreg_align_to         MIN_OUTLIER                                  \
            -volreg_align_e2a                                                     \
            -volreg_tlrc_warp                                                     \
            -align_opts_aea          -cost ${cost_a2e} -feature_size 0.5          \
                                     -partial_coverage -epi_strip 3dSkullStrip    \
                                     -giant_move -cmass cmass                     \
            -tlrc_base               ${refvol}                                    \
            -tlrc_NL_warp                                                         \
            -tlrc_NL_warped_dsets                                                 \
                ${odir_aw}/${subj}*_warp2std_nsu.nii.gz                           \
                ${odir_aw}/${subj}*_composite_linear_to_template.1D               \
                ${odir_aw}/${subj}*_shft_WARP.nii.gz                              \
            -regress_motion_per_run                                               \
            -regress_apply_mot_types  demean deriv                                \
            -regress_censor_motion    0.10                                        \
            -regress_censor_outliers  0.02                                        \
            -regress_est_blur_errts                                               \
            -regress_est_blur_epits                                               \
            -regress_run_clustsim     no                                          \
            -html_review_style        pythonic                                    \
            -execute

but this results in a proc script in which align_epi_anat.py is called like this:

align_epi_anat.py -anat2epi -anat subjGB7T_anat_ns+orig            \
       -suffix _al_junk                                            \
       -epi vr_base_min_outlier+orig -epi_base 0                   \
       -epi_strip 3dAutomask                                       \
       -anat_has_skull no                                          \
       -cost lpa+ZZ -feature_size 0.5 -partial_coverage -epi_strip \
       3dSkullStrip -giant_move -cmass cmass                       \
       -volreg off -tshift off

Note the -epi_strip occurs twice, and because the alignment fails (unlike in tests when I run align_epi_anat.py separately, see below for that script), I understand that the first option is used.

What am I doing wrong?

Testing align_epi_anat.py options (this gives me good alignment)

align_epi_anat.py -anat2epi 					\
	   -anat subjGB7T_anat_ns+orig   			\
       -epi zpad_vr_base+orig		\
       -epi_base 0               				\
       -suffix _al_edge_lpaZZ_SS_deobli_sep_partcov_gm_cc			\
       -epi_strip 3dSkullStrip         		\
       -anat_has_skull no        				\
       -cost lpa+ZZ -feature_size 0.5 			\
       -giant_move \
       -cmass cmass  \
       -volreg off -tshift off 		\
       -partial_coverage