Hi AFNI experts
I'm using afni_proc.py to do the preprocessing steps for my fMRI data. However, at the volreg step, a strange result like the image in the Attachment was exported. Only 2 subjects have this problem. And 1 of the 2 was solved by change another T1 file exported by dcm2nii (it exports 3 T1 files, *, o* and co*). I found that the problem first appear at rm.epi.nomask.r$run export by 3dAllineate at the volreg step (code below).
# apply catenated xform: volreg/epi2anat/tlrc
3dAllineate -base \
20190704_160705t1mpragesagisoTI1000waternos005a1001_ns+tlrc \
-input pb01.$subj.r$run.tshift+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-mast_dxyz 3 \
-prefix rm.epi.nomask.r$run

And the afni_proc.py code was also provided in case there is something wrong with it.

#!/usr/bin/env tcsh

# created by uber_subject.py: version 1.2 (April 5, 2018)
# creation date: Sun Nov 29 23:44:09 2020

# foreach subj_num (31 36 40 42 43 46 47 48 52 53 54 56 58 59 61 62 63 64 70 73 74 77 80 81)
foreach subj_num (48)
# set subject and group identifiers
set subj = S$subj_num
set gname = YNM

# set data directories
set top_dir = /data2/public_space/LZhang/audiovisual_orig_1st/data/fmri_newGLM
set anat_dir = $top_dir/raw_data/${subj}
set epi_dir = $top_dir/raw_data/${subj}
set stim_dir = $top_dir/time_file/${subj}

mkdir -p ${top_dir}/subject_results/group.${gname}/subj.${subj}/
cd ${top_dir}/subject_results/group.${gname}/subj.${subj}/

# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $anat_dir/20190704_160705t1mpragesagisoTI1000waternos005a1001.nii.gz \
-dsets \
$epi_dir/A1.nii.gz \
$epi_dir/A2.nii.gz \
$epi_dir/A3.nii.gz \
$epi_dir/A4.nii.gz \
$epi_dir/AV1.nii.gz \
$epi_dir/AV2.nii.gz \
$epi_dir/AV3.nii.gz \
$epi_dir/AV4.nii.gz \
-tcat_remove_first_trs 8 \
-tlrc_base MNI_avg152T1+tlrc \
-align_opts_aea -giant_move \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 6.0 \
-regress_stim_times \
$stim_dir/ba-8_A.txt \
$stim_dir/ba-8_AV.txt \
$stim_dir/ba0_A.txt \
$stim_dir/ba0_AV.txt \
$stim_dir/ba8_A.txt \
$stim_dir/ba8_AV.txt \
$stim_dir/da-8_A.txt \
$stim_dir/da-8_AV.txt \
$stim_dir/da0_A.txt \
$stim_dir/da0_AV.txt \
$stim_dir/da8_A.txt \
$stim_dir/da8_AV.txt \
$stim_dir/pa-8_A.txt \
$stim_dir/pa-8_AV.txt \
$stim_dir/pa0_A.txt \
$stim_dir/pa0_AV.txt \
$stim_dir/pa8_A.txt \
$stim_dir/pa8_AV.txt \
$stim_dir/ta-8_A.txt \
$stim_dir/ta-8_AV.txt \
$stim_dir/ta0_A.txt \
$stim_dir/ta0_AV.txt \
$stim_dir/ta8_A.txt \
$stim_dir/ta8_AV.txt \
-regress_stim_labels \
ba-8_A ba-8_AV ba0_A ba0_AV ba8_A ba8_AV da-8_A da-8_AV da0_A \
da0_AV da8_A da8_AV pa-8_A pa-8_AV pa0_A pa0_AV pa8_A pa8_AV ta-8_A \
ta-8_AV ta0_A ta0_AV ta8_A ta8_AV \
-regress_basis 'GAM' \
-regress_censor_motion 0.3 \
-regress_motion_per_run \
-regress_opts_3dD \
-jobs 50 \
-num_glt 12 \
-gltsym 'SYM: 0.25*ba-8_A +0.25*da-8_A +0.25*pa-8_A \
+0.25*ta-8_A' -glt_label 1 VI_-8 \
-gltsym 'SYM: 0.25*ba0_A +0.25*da0_A +0.25*pa0_A +0.25*ta0_A' \
-glt_label 2 VI_0 \
-gltsym 'SYM: 0.25*ba8_A +0.25*da8_A +0.25*pa8_A +0.25*ta8_A' \
-glt_label 3 VI_8 \
-gltsym 'SYM: 0.25*ba-8_AV +0.25*da-8_AV +0.25*pa-8_AV \
+0.25*ta-8_AV' -glt_label 4 VV_-8 \
-gltsym 'SYM: 0.25*ba0_AV +0.25*da0_AV +0.25*pa0_AV +0.25*ta0_AV' \
-glt_label 5 VV_0 \
-gltsym 'SYM: 0.25*ba8_AV +0.25*da8_AV +0.25*pa8_AV +0.25*ta8_AV' \
-glt_label 6 VV_8 \
-gltsym 'SYM: 0.0833*ba0_A +0.0833*ba-8_A +0.0833*ba8_A \
+0.0833*da0_A +0.0833*da-8_A +0.0833*da8_A +0.0833*pa0_A \
+0.0833*pa-8_A +0.0833*pa8_A +0.0833*ta0_A +0.0833*ta-8_A \
+0.0833*ta8_A' -glt_label 7 VI \
-gltsym 'SYM: 0.0833*ba0_AV +0.0833*ba-8_AV +0.0833*ba8_AV \
+0.0833*da0_AV +0.0833*da-8_AV +0.0833*da8_AV +0.0833*pa0_A \
+0.0833*pa-8_AV +0.0833*pa8_AV +0.0833*ta0_AV +0.0833*ta-8_AV \
+0.0833*ta8_AV' -glt_label 8 VV \
-gltsym 'SYM: 0.125*ba-8_A +0.125*da-8_A +0.125*pa-8_A \
+0.125*ta-8_A +0.125*ba-8_AV +0.125*da-8_AV +0.125*pa-8_AV \
+0.125*ta-8_AV' -glt_label 9 SNR-8 \
-gltsym 'SYM: 0.125*ba8_A +0.125*da8_A +0.125*pa8_A \
+0.125*ta8_A +0.125*ba8_AV +0.125*da8_AV +0.125*pa8_AV \
+0.125*ta8_AV' -glt_label 10 SNR0 \
-gltsym 'SYM: 0.125*ba0_A +0.125*da0_A +0.125*pa0_A +0.125*ta0_A \
+0.125*ba0_AV +0.125*da0_AV +0.125*pa0_AV +0.125*ta0_AV' -glt_label \
11 SNR8 \
-gltsym 'SYM: 0.0833*ba0_AV +0.0833*ba-8_AV +0.0833*ba8_AV \
+0.0833*da0_AV +0.0833*da-8_AV +0.0833*da8_AV +0.0833*pa0_A \
+0.0833*pa-8_AV +0.0833*pa8_AV +0.0833*ta0_AV +0.0833*ta-8_AV \
+0.0833*ta8_AV -0.0833*ba0_A -0.0833*ba-8_A -0.0833*ba8_A \
-0.0833*da0_A -0.0833*da-8_A +0.0833*da8_A -0.0833*pa0_A \
-0.0833*pa-8_A -0.0833*pa8_A -0.0833*ta0_A -0.0833*ta-8_A \
-0.0833*ta8_A' -glt_label 12 VV-VI \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts

tcsh -xef proc.$subj |& tee output.proc.$subj

end

Could anyone help me and thanks in advance!

regards,
Lei Zhang