Dear AFNI experts,

I ran align_epi_anat.py below which generated align_tlrc.jpg attached. For this, both anat (T1) and epi files were generated as tlrc format.

align_epi_anat.py \
-epi2anat \
-anat T1w_acpc_dc_restore.nii.gz \
-epi ${subj}_REST1_LR+orig\
-epi_base 0 \
-volreg off \
-cost lpa+ZZ \
-big_move \
-overwrite

Therefore, when running run the proc.py , it showed the error below, which is the same as here (https://afni.nimh.nih.gov/afni/community/board/read.php?1,160486)

3dbucket -prefix subj_T1.nii.gz
++ 3dbucket: AFNI version=AFNI_19.0.06 (Feb 4 2019) [64-bit]
** ERROR: output dataset name 'subj_T1.nii.gz' conflicts with existing file
** ERROR: dataset NOT written to disk!

Here is the proc py script I used.

afni_proc.py \
-blocks despike align tlrc blur mask regress \
-copy_anat /Volumes/Elements/RS/${subj}/sub_T1.nii.gz \
-anat_follower_ROI aaseg anat /Volumes/Elements/RS/${subj}/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI aeseg epi /Volumes/Elements/RS/${subj}/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI FSvent epi /Volumes/Elements/RS/${subj}/vent.nii.gz \
-anat_follower_ROI FSWm epi /Volumes/Elements/RS/${subj}/wm.nii.gz \
-anat_follower_erode FSvent FSWm \
-dsets /Volumes/Elements/RS/8/${subj}/${subj}_REST+orig \
-out_dir Proc_results_R2LR \
-script py_result_${subj}_script \
-scr_overwrite \
-subj_id ${subj}_V1_MR \
-align_opts_aea -cost lpa -cost lpa+ZZ -giant_move \
-tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-tlrc_NL_awpy_rm no \
-tlrc_no_ss \
-regress_apply_mask \
-regress_ROI_PC FSvent 3 \
-regress_make_corr_vols aeseg FSvent \
-regress_anaticor_fast \
-regress_anaticor_label FSWm \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts


According to the suggestion from RIck in this thread (https://afni.nimh.nih.gov/afni/community/board/read.php?1,160486), I changed the view to orig using this command line: setenv AFNI_NIFTI_VIEW orig

After that when running align_epi_anat.py using the same script, the alignment of the anat (T1) and epi files in orig are not as good as tlrc. (attached files including align orig_1). Could you please advise how to resolve this issue?

Best,
JW