Thank you for your time and help in advance!

I have started to analyze a new research study using the afni_proc.py script. I have used the same script (with minor modifications for names on several other datasets). I have included the script that we are using below. When I went to check the pre-processed images. I cannot get the functional images to overlay on the mprage (even after they have been "aligned"). Specifically, the mprage shows up in the center of the image screen and the functional appears in the bottom right hand corner. Please note, that I do get an obliquity warning; however, I am fairly certain that this has nothing to do with my problem. The only difference between this study and the previous ones that I have worked on is that this study uses an axial mprage (vs sagittal in others). I am wondering if the issue is that these were taken axially or if there is possibly something wrong with the information in the image headers or in the alignment process itself. Please help me figure out what dumb mistake I am making.

Thanks,

Corrie


#!/bin/tcsh

#Run script from Volumes/FiezData/rrf/hf_proc/lea

foreach subj (01 02 03 04 10 11 12 13 16 18 20 21 23 24)

afni_proc.py -copy_anat hf${subj}/structs/hf${subj}_mprage_ss+orig. \
-dsets hf${subj}/functs/hf${subj}_run1+orig \
hf${subj}/functs/hf${subj}_run2+orig \
hf${subj}/functs/hf${subj}_run3+orig \
hf${subj}/functs/hf${subj}_run4+orig \
-blocks tshift align tlrc volreg blur mask scale regress \
-move_preproc_files \
-out_dir hf${subj}_localizer_allruns \
-outlier_count yes \
-script hf${subj}_preproc_script \
-sep_char _ -subj_curly -subj_id ${subj} -verb 3 \
-tcat_remove_first_trs 2 \
-tshift_align_to -slice 14 -tshift_interp -Fourier \
-tshift_opts_ts -tpattern alt+z \
-align_opts_aea \
-big_move \
-AddEdge -anat_has_skull no \
-volreg_tlrc_warp -volreg_zpad 4 -volreg_align_e2a \
-blur_filter -1blur_fwhm -blur_size 5.5 -scale_max_val 200 \
-regress_stim_times designfiles/hf${subj}_stimtimes.*.1D\
-regress_stim_labels houses faces words letters patterns \
-regress_basis 'BLOCK(18,1)' \
-regress_est_blur_errts \
-regress_opts_3dD \
-gltsym 'SYM: +houses -patterns' -glt_label 1 housesVpatterns \
-gltsym 'SYM: +words -patterns' -glt_label 2 wordsVpatterns \
-gltsym 'SYM: +faces -patterns' -glt_label 3 facesVpatterns \
-gltsym 'SYM: +words +letters -patterns' -glt_label 4 alphabeticVpatterns

end
end