Dear colleagues,

I would appreciate any advice on how to fix wrong anatomical image after skull stripping or alignment (I am not share what causes such distortion and rotation). The initial anatomical and fMRI images are Ok. However, after alignment final_anat becomes distorted and rotated. This is the only subject out of 60 that has such a problem.

The script I implemented:

afni_proc.py -subj_id $subj
-script proc.$subj -scr_overwrite \
-blocks despike tshift align tlrc volreg \
blur mask scale regress \
-copy_anat $anat_dir/${subj}_T1w.nii.gz \
-dsets \
$epi_dir/${subj}_task-pmt_run-01_bold.nii.gz \
$epi_dir/${subj}_task-pmt_run-02_bold.nii.gz \
$epi_dir/${subj}_task-pmt_run-03_bold.nii.gz \
-tcat_remove_first_trs 0 \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
-tlrc_base MNI_avg152T1+tlrc \
-tlrc_opts_at -init_xform AUTO_CENTER \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 8.0 \
-regress_stim_times \
$epi_dir/cross.1D \
$epi_dir/ADD1.1D \
…….
$epi_dir/CON3.1D \
-regress_stim_labels \
cross ADD1……CON3 \
-regress_stim_types AM1 \
-regress_basis_multi dmBLOCK \
-regress_motion_per_run \
-regress_censor_motion 0.5 \
-regress_censor_outliers 0.1 \
-regress_compute_fitts \
-regress_opts_3dD -jobs 2 -num_glt 30 \
-gltsym 'SYM: ADD1 -cross' -glt_label 1 ADD1-cross \
…..
-gltsym 'SYM: CON2 -CON3' -glt_label 30 CON3-CON3 \
-regress_3dD_stop \
-regress_reml_exec \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-html_review_style pythonic

Thank you in advance!

Sincerely,
Asya Istomina