Hi there,
My afni_proc.py file is having difficulty with opening one of my stimulus files.
When I ran the file_tool code, it indicated there were no "bad characters". Any other suggestions I can try?
Thank you very much
file_tool -test -infile Instruct.txt
Instruct.txt has 0 bad characters
Instruct.txt file type: DOS
consider: file_tool -show_file_type -infile Instruct.txt -prefix FIXED.txt
tcsh -xef AfniProc
afni_proc.py -subj_id 1423 -script proc.Dec5_2020 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /imaging/Tamara/Youth/1423/1423.anat+orig -dsets /imaging/Tamara/Youth/1423/1423.1+orig.HEAD /imaging/Tamara/Youth/1423/1423.2+orig.HEAD /imaging/Tamara/Youth/1423/1423.3+orig.HEAD /imaging/Tamara/Youth/1423/1423.4+orig.HEAD /imaging/Tamara/Youth/1423/1423.5+orig.HEAD /imaging/Tamara/Youth/1423/1423.6+orig.HEAD -tcat_remove_first_trs 0 -tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp -volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 -regress_stim_times /imaging/Tamara/Youth/1423/Dfeel_Bad_NoResp.txt /imaging/Tamara/Youth/1423/Dfeel_Bad_Resp.txt /imaging/Tamara/Youth/1423/Dfeel_Happy_NoResp.txt /imaging/Tamara/Youth/1423/Dfeel_Happy_Resp.txt /imaging/Tamara/Youth/1423/Feel_Bad_NoResp.txt /imaging/Tamara/Youth/1423/Feel_Bad_Resp.txt /imaging/Tamara/Youth/1423/Feel_Happy_NoResp.txt /imaging/Tamara/Youth/1423/Feel_Happy_Resp.txt /imaging/Tamara/Youth/1423/Nat_neg_NoResp.txt /imaging/Tamara/Youth/1423/Nat_neg_Resp.txt /imaging/Tamara/Youth/1423/Nat_post_NoResp.txt /imaging/Tamara/Youth/1423/Nat_post_Resp.txt /imaging/Tamara/Youth/1423/Rating.txt /imaging/Tamara/Youth/1423/Instruct.txt -regress_stim_labels Dfeel_Bad_NoResp Dfeel_Bad_Resp Dfeel_Happy_NoResp Dfeel_Happy_Resp Feel_Bad_NoResp Feel_Bad_Resp Feel_Happy_NoResp Feel_Happy_Resp Nat_neg_NoResp Nat_neg_Resp Nat_post_NoResp Nat_post_Resp Rating Instruct -regress_basis dmBLOCK -regress_stim_types AM1 -regress_censor_motion 1.0 -regress_censor_outliers 0.1 -regress_apply_mot_types demean deriv -regress_motion_per_run -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -execute
-- will use min outlier volume as motion base
-- tcat: reps is now 366
++ updating polort to 3, from run len 366.0 s
-- using non-linear template alignment
-- volreg: using base dset vr_base_min_outlier+orig
++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 2.5 mm tlrc voxels
-- applying anat warps to 1 dataset(s): 1423.anat
-- masking: group anat = 'MNI152_T1_2009c+tlrc', exists = 1
-- have 1 ROI dict entries ...
++ applying 14 stim types: ['AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1', 'AM1']
-- will apply motion types: demean, deriv
** warnings for global stim_times format of file /imaging/Tamara/Youth/1423/Dfeel_Bad_NoResp.txt
- negative stim time -1
- has repeated times
** warnings for global stim_times format of file /imaging/Tamara/Youth/1423/Dfeel_Happy_NoResp.txt
- negative stim time -1
- has repeated times
** warnings for global stim_times format of file /imaging/Tamara/Youth/1423/Feel_Bad_NoResp.txt
- negative stim time -1
- has repeated times
** warnings for global stim_times format of file /imaging/Tamara/Youth/1423/Feel_Happy_NoResp.txt
- negative stim time -1
- has repeated times
** warnings for global stim_times format of file /imaging/Tamara/Youth/1423/Nat_neg_NoResp.txt
- negative stim time -1
- has repeated times
** unusable token, bad floats : .4:
line = .4: .9 18.6: .9 35.9: .9 56.1: .9 73.4: .9 89.6: .9 107.9: .9 131.6: .9 151.9: .9 168.1: .9 191.9: .9 209.1: .9 225.4: .9 248.1: .9 266.4: .9 283.6: .9 301.9: .9 323.1: .9 *
** A1D: failed to read data file /imaging/Tamara/Youth/1423/Instruct.txt
** failed to load stimulus timing file '/imaging/Tamara/Youth/1423/Instruct.txt'
-- consider use of '-test_stim_files no' if files are OK
------------------------------------------------------------
** script creation failure for block 'regress'
+- consider use of: -html_review_style pythonic
----------------------------------------------------------------------
** failed command (create_script):
afni_proc.py -subj_id 1423 -script proc.Dec5_2020 -scr_overwrite -blocks \
tshift align tlrc volreg blur mask scale regress -copy_anat \
/imaging/Tamara/Youth/1423/1423.anat+orig -dsets \
/imaging/Tamara/Youth/1423/1423.1+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.2+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.3+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.4+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.5+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.6+orig.HEAD -tcat_remove_first_trs 0 \
-tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp -volreg_align_to \
MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 \
-regress_stim_times /imaging/Tamara/Youth/1423/Dfeel_Bad_NoResp.txt \
/imaging/Tamara/Youth/1423/Dfeel_Bad_Resp.txt \
/imaging/Tamara/Youth/1423/Dfeel_Happy_NoResp.txt \
/imaging/Tamara/Youth/1423/Dfeel_Happy_Resp.txt \
/imaging/Tamara/Youth/1423/Feel_Bad_NoResp.txt \
/imaging/Tamara/Youth/1423/Feel_Bad_Resp.txt \
/imaging/Tamara/Youth/1423/Feel_Happy_NoResp.txt \
/imaging/Tamara/Youth/1423/Feel_Happy_Resp.txt \
/imaging/Tamara/Youth/1423/Nat_neg_NoResp.txt \
/imaging/Tamara/Youth/1423/Nat_neg_Resp.txt \
/imaging/Tamara/Youth/1423/Nat_post_NoResp.txt \
/imaging/Tamara/Youth/1423/Nat_post_Resp.txt \
/imaging/Tamara/Youth/1423/Rating.txt \
/imaging/Tamara/Youth/1423/Instruct.txt -regress_stim_labels \
Dfeel_Bad_NoResp Dfeel_Bad_Resp Dfeel_Happy_NoResp Dfeel_Happy_Resp \
Feel_Bad_NoResp Feel_Bad_Resp Feel_Happy_NoResp Feel_Happy_Resp \
Nat_neg_NoResp Nat_neg_Resp Nat_post_NoResp Nat_post_Resp Rating \
Instruct -regress_basis dmBLOCK -regress_stim_types AM1 \
-regress_censor_motion 1.0 -regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv -regress_motion_per_run \
-regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \
-regress_est_blur_errts -regress_run_clustsim no -execute
