Hi Experts,

Below is a copy of the script I used to run our imagery task as well as the terminal output. Your guidance would be appreciated to help discover the reason for the error "script creation failure for block 'regress'". I am using Version AFNI_2011_12_21_1014.

Thanks for your time!

Jessica

****************************************************SCRIPT***********************************************************

#!/bin/tcsh

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

set study = PTSD_Conditioning

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

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

cd /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Linear_Imagery

foreach subject (sub11)

afni_proc.py \
-subj_id ${subject} \
-script ${scriptfolder}/${subject}_imagery_linear_proc_script \
-out_dir ${subfolder}/${subject}/${subject}.imagery_linear.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 \
-do_block align tlrc \
-tcat_remove_first_trs 3 \
-volreg_align_to third \
-volreg_align_e2a \
-volreg_tlrc_warp \
-regress_stim_times 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 \
-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)' \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_opts_3dD \
-gltsym 'SYM: +im_neut_recall -im_neut_base' -glt_label 1 im_neutrecall_vs_base \
-gltsym 'SYM: +im_trauma_recall -im_trauma_base' -glt_label 2 im_traumarecall_vs_base \
-gltsym 'SYM: +im_neut_rest -im_neut_base' -glt_label 3 im_neutrest_vs_base \
-gltsym 'SYM: +im_trauma_rest -im_trauma_base' -glt_label 4 im_traumarest_vs_base \
-gltsym 'SYM: +im_trauma_recall -im_neut_recall' -glt_label 5 im_traumarecall_vs_neutrecall \
-gltsym 'SYM: +im_trauma_rest -im_neut_rest' -glt_label 6 im_traumarest_vs_neutrest \
-gltsym 'SYM: +im_trauma_script -im_neut_script' -glt_label 7 im_traumascript_vs_neutscript \
-gltsym 'SYM: +im_trauma-base -im_neut_base' -glt_label 8 im_traumabase_vs_neutbase \
-jobs 4 \
-regress_run_clustsim no \
-regress_est_blur_epits \
-regress_est_blur_errts

tcsh -xef ${scriptfolder}/${subject}_imagery_linear_proc_script |$ tee ${scriptfolder}/output.${subject}_imagery_linear_proc_script

end


****************************************************OUTPUT***********************************************************

warning: removing first 3 TRs from beginning of each run
--> the stimulus timing files must reflect the removal of these TRs
-- tcat: reps is now 270
-- volreg: base/sub indices are 0, 2
++ volreg: warp and align to isotropic 3.5 mm tlrc voxels
-- masking: group anat = 'TT_N27+tlrc', exists = 1
++ updating polort to 4, from run len 540.0 s
** error: have 8 basis functions but 1 stim classes
** script creation failure for block 'regress'
----------------------------------------------------------------------
** failed command (create_script):

afni_proc.py -subj_id sub11 -script \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Linear_Imagery/sub11_imagery_linear_proc_script \
-out_dir \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery_linear.results \
-dsets \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Neutral+orig.HEAD \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Trauma+orig.HEAD \
-copy_anat \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/p532/e542/sub11.PTSD_Conditioning.spgr+orig \
-do_block align tlrc -tcat_remove_first_trs 3 -volreg_align_to third \
-volreg_align_e2a -volreg_tlrc_warp -regress_stim_times \
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 -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)' -regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 -regress_opts_3dD -gltsym 'SYM: \
+im_neut_recall -im_neut_base' -glt_label 1 im_neutrecall_vs_base \
-gltsym 'SYM: +im_trauma_recall -im_trauma_base' -glt_label 2 \
im_traumarecall_vs_base -gltsym 'SYM: +im_neut_rest -im_neut_base' \
-glt_label 3 im_neutrest_vs_base -gltsym 'SYM: +im_trauma_rest \
-im_trauma_base' -glt_label 4 im_traumarest_vs_base -gltsym 'SYM: \
+im_trauma_recall -im_neut_recall' -glt_label 5 \
im_traumarecall_vs_neutrecall -gltsym 'SYM: +im_trauma_rest \
-im_neut_rest' -glt_label 6 im_traumarest_vs_neutrest -gltsym 'SYM: \
+im_trauma_script -im_neut_script' -glt_label 7 \
im_traumascript_vs_neutscript -gltsym 'SYM: +im_trauma-base \
-im_neut_base' -glt_label 8 im_traumabase_vs_neutbase -jobs 4 \
-regress_run_clustsim no -regress_est_blur_epits -regress_est_blur_errts
----------------------------------------------------------------------
$: Command not found.
/media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Linear_Imagery/sub11_imagery_linear_proc_script: No such file or directory.



Edited 1 time(s). Last edit at 09/10/2015 03:46PM by lindsle6.