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
