Hi Experts,

I am trying to run a script (see below) and it keeps skipping over the Non-Linear Warp, and is ignoring the timing files. It also creates "No_STATS" and "No_DSET" like it were resting data (but it's NOT resting data.) I am using Version AFNI_2011_12_21_1014.

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#This script is designed for running multiple subjects without stopping between running
#afni_proc.py and starting the script generated by afni_proc.py.

#Sets the folder containing the subject data

setenv subfolder /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data

setenv scriptfolder /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery

setenv timing_files /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery/Timing_Files

#Creates a variable called "study" and sets its value.

set study = PTSD_Conditioning

#Opens the scripts directory

cd /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery

#Sets a list variable called "subject" and runs afni_proc.py for each subject in the list
#
#ALL SUBJECTS foreach subject (sub11 sub65 sub122 sub124 sub132 sub296 sub308 sub329 sub350 sub370 sub402 sub425 sub519 sub530 sub531 sub538 sub541 sub546 sub557 sub574 sub577 sub612 sub629 sub642 sub669 sub699 sub717 sub727 sub731 sub755)

foreach subject (sub11)

########################################################################################
#Starts the afni_proc.py python script to create a single subject pre-processing script#
########################################################################################

afni_proc.py \
-subj_id ${subject} \
-script ${scriptfolder}/${subject}_imagery_proc_script \
-out_dir ${subfolder}/${subject}/${subject}.imagery.results \
-dsets ${subfolder}/${subject}/${subject}.${study}.Neutral+orig.HEAD \
${subfolder}/${subject}/${subject}.${study}.Trauma+orig.HEAD \
-copy_anat /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/p532/e542/sub11.PTSD_Conditioning.spgr+orig
#-copy_anat ${subfolder}/${subject}/p*/e*/${subject}.${study}.spgr+orig \
-anat_has_skull yes \
-do_block align tlrc \
-tcat_remove_first_trs 3 \
#Puts the brain in MNI space instead of TT_N27 tailarach space
-tlrc_base ${scriptfolder}/MNI152_T1_1mm_brain.nii \
#Do non-linear warping
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 4 \
#Apply mask to 3dDeconvolve??
-regress_stim_times ${timing_files}/imagery_stim_times.*.1D \
-regress_stim_labels im_neut_base im_neut_script im_neut_recall im_neut_rest \
im_trauma_base im_trauma_script im_trauma_recall im_trauma_rest \
#PREVIOUSLY DID NOT ADD THIS. Previously afni_proc.py chose the 'GAM' option for our stimulus timing files
-regress_basis_multi 'BLOCK(60,1)' 'BLOCK(30,1)' 'BLOCK(30,1)' 'BLOCK(60,1)' \
'BLOCK(60,1)' 'BLOCK(30,1)' 'BLOCK(30,1)' 'BLOCK(60,1)' \
#Censors TRs with more than 0.3mm motion
-regress_censor_motion 0.3 \
#Censors TRs when more than 10% of the automasked brain are outliers
-regress_censor_outliers 0.1 \
-regress_opts_3dD \
-gltsym 'SYM: +im_neut_recall -im_neut_base' -glt_label 1 im_neut_recall_vs_base \
-gltsym 'SYM: +im_trauma_recall -im_trauma_base' -glt_label 2 im_trauma_recall_vs_base \
-gltsym 'SYM: +im_neut_rest -im_neut_base' -glt_label 3 im_neut_rest_vs_base \
-gltsym 'SYM: +im_trauma_rest -im_trauma_base' -glt_label 4 im_trauma_rest_vs_base \
-gltsym 'SYM: +im_neut_script -im_neut_base' -glt_label 5 im_neut_script_vs_base \
-gltsym 'SYM: +im_trauma_script -im_trauma_base' -glt_label 6 im_trauma_script_vs_base \
-gltsym 'SYM: +im_trauma_recall -im_neut_recall' -glt_label 7 im_trauma_recall_vs_neut_recall \
-gltsym 'SYM: +im_trauma_rest -im_neut_rest' -glt_label 8 im_trauma_rest_vs_neut_rest \
-gltsym 'SYM: +im_trauma_script -im_neut_script' -glt_label 9 im_trauma_script_vs_neut_script \
-gltsym 'SYM: +im_trauma_base -im_neut_base' -glt_label 10 im_trauma_base_vs_neut_base \
#-jobs 4 \
-regress_est_blur_epits \
-regress_est_blur_errts

#Runs the script generated by afni_proc.py for this subject
tcsh -xef ${scriptfolder}/${subject}_imagery_proc_script |& tee ${scriptfolder}/output.${subject}_imagery_proc_script

end
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Your opinion is very valuable!

Thanks for your time,

Jessica