Hello,

I am having great difficulty in aligning the EPI to the anatomical for one of my participants. In original space, they are aligned quite well, but after warping it comes out off. I've tried numerous different cost functions to no avail. I've attached some screenshots I hope will demonstrate this. These are using the cost function lpc, which thus far seems to result in the best alignment. I've also tried using the various "move" functions ('big_move' etc.), none of which have helped. There doesn't seem to be anything unusual about this participant, which is why it is puzzling me. I've pasted my processing scripts below. Please let me know if any other information would be helpful. I will take any suggestions you may have.

Thanks,
Kara


@Align_Centers \
-cm \
-prefix $subj.anat.uni.ac \
-dset $scan_dir/$subj.anat.uni+orig \
-base TT_N27_SSW.nii.gz

@SSwarper \
-input $scan_dir/$subj.anat.uni.ac+orig \
-base TT_N27_SSW.nii.gz \
-subid $subj \
-unifize_off

afni_proc.py -subj_id $subj.$task \
-script $subj.$task.data_prep -scr_overwrite \
-out_dir $task_dir/imaging_data/subjects/$subj/$scan_dir \
-copy_anat $top_dir/anatSS.$subj.nii \
-anat_has_skull no \
-anat_follower anat_w_skull anat $top_dir/$subj.anat.uni.ac+orig \
-dsets pb00.$subj.$task+orig.HEAD \
-blocks tcat despike ricor tshift align tlrc volreg blur mask scale regress \
-radial_correlate_blocks tcat volreg \
-tcat_remove_first_trs 3 \
-ricor_regs_nfirst 3 \
-ricor_regs $top_dir/$subj.$task.RVT.1D \
-align_opts_aea -check_flip -cmass cmass \
-tlrc_base TT_N27_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets $top_dir/anatQQ.$subj.nii \
$top_dir/anatQQ.$subj.aff12.1D \
$top_dir/anatQQ.{$subj}_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_warp_dxyz 1.75 \
-mask_epi_anat yes \
-blur_size 6 \
-regress_apply_ricor yes \
-regress_stim_times \
$stim_dir/listen_p.1D \
$stim_dir/count.1D \
$stim_dir/respond_p.1D \
-regress_stim_labels \
listen count respond \
-regress_basis 'BLOCK(40,1)' \
-regress_opts_3dD \
-local_times \
-jobs 8 \
-regress_apply_mot_types demean deriv \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.05 \
-regress_reml_exec \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no