Hello,
I am checking the alignment between the final anatomical and the full mask for each participant to ensure that coverage is appropriate. I have a couple of instances where the coverage is really off and others where some voxels appear around the actual brain.
What may I do to improve the coregistration? Finally, how much off is acceptable? For example, would sub-020 in the picture be considered OK or would you preprocess differently?
My current proc.py is
afni_proc.py -subj_id $subj_id \
-blocks tshift align tlrc volreg blur mask scale \
regress \
-copy_anat $data_root/$subj_id/$session/anat/sub-0??_ses-T?_T1w.nii.gz \
-dsets \
$data_root/$subj_id/$session/func/sub-0??_ses-T?_task-Num_run-0?_bold.nii.gz \
-align_opts_aea -cost lpc+ZZ \
-tshift_interp -quintic \
-tlrc_base HaskinsPeds_NL_template1.0+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-regress_motion_per_run \
-regress_censor_motion 0.6 \
-regress_censor_outliers 0.1 \
-regress_censor_prev no \
-regress_reml_exec \
-regress_stim_times \
$data_root/$subj_id/$session/stim/Easy.* \
$data_root/$subj_id/$session/stim/Medium.* \
$data_root/$subj_id/$session/stim/Hard.* \
$data_root/$subj_id/$session/stim/control_n.* \
-regress_stim_labels \
LargeD MediumD SmallD Ctrl_n \
-regress_basis GAM \
-regress_opts_3dD \
-bout \
-jobs 4 \
-gltsym 'SYM: SmallD -LargeD' -glt_label 1 Small-Large \
-gltsym 'SYM: SmallD -MediumD' -glt_label 2 Small-Medium \
-gltsym 'SYM: MediumD -LargeD' -glt_label 3 Medium-Large \
-gltsym 'SYM: SmallD MediumD LargeD -3*Ctrl_n' -glt_label 4 All-control \
-gltsym 'SYM: LargeD -Ctrl_n' -glt_label 5 Large-Control \
-gltsym 'SYM: SmallD -Ctrl_n' -glt_label 6 Small-Control \
-gltsym 'SYM: MediumD -Ctrl_n' -glt_label 7 Medium-Control \
-regress_est_blur_epits \
-regress_est_blur_errts \
-write_3dD_prefix stats.MoreContrasts \
-execute
Thank you!