Thanks. Was obvious once you pointed it out. Scripting is always an on going education(read here: pain *laugh*) for us psychology types. But the more I read and understand this python script the more glad I am to be learning it now for future work.
However, for the sake of time on this fast approaching project can you confirm there is no -argument such as -regress_bandpass built into 3dDeconvolve since I have all that scripting already laid out and working.
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Returning to our afni_proc.py testing, I am running into this newer error:
** error: option -regress_stim_labels follows unknown arg #34 (/Volumes/Motion_Pre-moco/2H_s4+orig_vr_motion.1D[0])
Not sure why it is considering it a program arugment rather then a .1D file name. Let me know if anything in script below explains this.
Will afni_proc be able to utilize my external_censor file if it is a concatenation of all 6 sessions? Or do I need to feed it individual ones for each session.
foreach subj ( 2H )# 5U 6T 7U 8K 9S 10H 12N 13B 14K 15U 16Y 17M 18O )
cd ${subj}
foreach sess ( s4 s5 s6 s7 s8 s9 )
afni_proc.py -dsets ${subj}_*_vr_zp4_cardnudg_e2a_FWHM+tlrc.HEAD \
-out_dir /Volumes/Spock_HD/Dane_FC/FC_DATA_Task1/ICN_Runs \
-blocks scale regress \
-regress_censor_extern $censorfile/${subj}_autocensor_AC3VC_pre-moco.1D \
-regress_polort 3 \
-regress_basis 'TENT(2.5,17.5,7)' \
-regress_local_times \
-regress_stim_files 1 $stimdir/${subj}_Strong_stim4b.1D -regress_stim_labels 1 'Strg' \
-regress_stim_files 2 $stimdir/${subj}_Weak_stim4b.1D -regress_stim_labels 2 'Weak' \
-regress_motion_file 3 /Volumes/Motion_Pre-moco/${subj}_${sess}+orig_vr_motion.1D'[0]' -regress_stim_labels 3 'roll' \
-regress_motion_file 4 /Volumes/Motion_Pre-moco/${subj}_${sess}+orig_vr_motion.1D'[1]' -regress_stim_labels 4 'pitch' \
-regress_motion_file 5 /Volumes/Motion_Pre-moco/${subj}_${sess}+orig_vr_motion.1D'[2]' -regress_stim_labels 5 'yaw' \
-regress_motion_file 6 /Volumes/Motion_Pre-moco/${subj}_${sess}+orig_vr_motion.1D'[3]' -regress_stim_labels 6 'x' \
-regress_motion_file 7 /Volumes/Motion_Pre-moco/${subj}_${sess}+orig_vr_motion.1D'[4]' -regress_stim_labels 7 'y' \
-regress_motion_file 8 /Volumes/Motion_Pre-moco/${subj}_${sess}+orig_vr_motion.1D'[5]' -regress_stim_labels 8 'z' \
-regress_bandpass 0.008 0.07 \
-regress_make_cbucket yes \
-regress_errts_prefix ${subj}_${sess}_prepro_bp07 \
end
end
Thank you so much for your patience and help. No one in my lab has really taken up afni_proc so I am trouble shooting and testing all on my own. Your responses are really invaluable.
~`Dane
