Hi Rick,

I am still trying to make sense of what is most appropriate for the 3dQwarp. Ideally, I will use this to nonlinearly warp the anatomy to a 1mm^3 MNI template and then the epi to the MNI warped anatomy. Since I used the proc.py for all pre-processing I am a bit confused as to what files to use from the output.

It seems from a line of code I have received for 3dQwarp (which I can't get to work yet and is a separate issue), it assumes I have not aligned any EPI to anatomy...So I may want to remove that step as well from the below afni_proc.py script I have been using since I plan to use the nonlinear warp to do this later.

Thanks,

danny


afni_proc.py \
-subj_id ${subject} \
-script proc_${subject}.WMC_OurModel_Correct_Trials_3 \
-out_dir ${subfolder}/${subject}/${subject}.WMC_OurModel_Correct_Trials.results_3 \
-dsets ${subfolder}/${subject}/${subject}.${study}.WMC1+orig.HEAD \
${subfolder}/${subject}/${subject}.${study}.WMC2+orig.HEAD \
${subfolder}/${subject}/${subject}.${study}.WMC3+orig.HEAD \
${subfolder}/${subject}/${subject}.${study}.WMC4+orig.HEAD \
-copy_anat ${subfolder}/${subject}/${subject}.${study}.spgr+orig \
-do_block align \
-tcat_remove_first_trs 3 \
-volreg_align_to first \
-volreg_align_e2a \
-blur_size 6 \
-regress_stim_times ${timing_files}/${subject}/Ignore_Cue.1D ${timing_files}/${subject}/Remember_Cue.1D ${timing_files}/${subject}/NT1_array_onset.1D ${timing_files}/${subject}/NT1FT1_array_onset.1D ${timing_files}/${subject}/NT2_array_onset.1D ${timing_files}/${subject}/NT1FD1_array_onset.1D ${timing_files}/${subject}/NT1ND1_array_onset.1D ${timing_files}/${subject}/Probe.1D \
-regress_stim_labels Ignore_Cue Remember_All_Cue NT1_array_onset NT1FT1_array_onset NT2_array_onset NT1FD1_array_onset NT1ND1_array_onset Probe_onset \
-regress_basis_multi 'GAM' 'GAM' 'GAM(8.6,.547,2.5)' 'GAM(8.6,.547,2.5)' 'GAM(8.6,.547,2.5)' 'GAM(8.6,.547,2.5)' 'GAM(8.6,.547,2.5)' 'GAM' \
-regress_opts_3dD \
-local_times \
-GOFORIT 9 \
-gltsym 'SYM: +Ignore_Cue -Remember_All_Cue' -glt_label 1 Ignore_vs_RememberAll \
-gltsym 'SYM: +NT2_array_onset -NT1_array_onset' -glt_label 2 NT2_array_vs_NT1_array \
-gltsym 'SYM: +NT1ND1_array_onset -NT1_array_onset' -glt_label 3 NT1ND1_array_vs_NT1_array \
-gltsym 'SYM: +NT1FD1_array_onset -NT1_array_onset' -glt_label 4 NT1FD1_array_vs_NT1_array \
-gltsym 'SYM: +NT1ND1_array_onset -NT2_array_onset' -glt_label 5 NT1ND1_array_vs_NT2_array \
-gltsym 'SYM: +NT1FD1_array_onset -NT1FT1_array_onset' -glt_label 6 NT1FD1_array_vs_NT1FT1_array \
-gltsym 'SYM: +NT1FT1_array_onset -NT1FD1_array_onset' -glt_label 7 NT1FT1_array_vs_NT1FD1_array \
-gltsym 'SYM: +NT1FT1_array_onset -NT1_array_onset' -glt_label 8 NT1FT1_array_vs_NT1_array \
-gltsym 'SYM: +NT1FT1_array_onset -NT2_array_onset' -glt_label 9 NT1FT1_array_vs_NT2_array \
-gltsym 'SYM: +NT1FD1_array_onset -NT1ND1_array_onset' -glt_label 10 NT1FD1_array_vs_NT1ND1_array \
-jobs 10 \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-no_epi_review

tcsh -xef proc_${subject}.WMC_OurModel_Correct_Trials_3|& tee output.proc_${subject}.WMC_OurModel_Correct_Trials_3