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yk40_
June 09, 2021 04:37PM
Dear AFNI experts,

I developed an afni_proc.py script for my project and tested it on my first subject, but am receiving errors. I am also receiving the same errors when testing the script on another subject. Please note, to get the different files needed as input into my afni_proc.py script, I first completed the following: I used dcm2niix to convert both the structural file and the functional file of my subject from .dcm to .nii.gz format. Then, I ran @Align_Centers to align the structural file’s center to the center of MNI152_2009_template_SSW.nii.gz, and next, I ran @Align_Centers to align the functional file’s center to the center of MNI152_2009_template_SSW.nii.gz. Finally, I ran @SSWarper, with the input being the aligned/“shifted” structural file (which was the output from running @Align_Centers on the structural file), and the base being MNI152_2009_template_SSW.nii.gz. All the files used as input into my afni_proc.py script do exist in the paths indicated by my afni_proc.py script.

Could you please see the below script and error outputs and suggest how I might be able to get afni_proc.py to work?

My afni_proc.py script:
afni_proc.py \
-subj_id AES101_Exercise \
-copy_anat Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatSS.AES101.nii \
-anat_has_skull no \
-anat_follower anat_w_skull anat Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXanat_shft.nii.gz \
-dsets Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXpicviewing_shft.nii.gz \
-blocks tshift align tlrc volreg blur mask scale regress \
-radial_correlate_blocks tcat volreg \
-tcat_remove_first_trs 2 \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.nii \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.aff12.1D \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_epi_anat yes \
-blur_size 4.0 \
-regress_stim_times Volumes/E4BHData/stimtimes/neutral.1D Volumes/E4BHData/stimtimes/pleasant.1D Volumes/E4BHData/stimtimes/unpleasant.1D \
-regress_stim_labels neutral pleasant unpleasant \
-regress_basis 'BLOCK(20,1)' \
-regress_opts_3dD \
-jobs 4 \
-gltsym 'SYM: pleasant -neutral' \
-glt_label 1 P-N \
-gltsym 'SYM: unpleasant -neutral' \
-glt_label 2 U-N \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.05 \
-regress_3dD_stop \
-regress_reml_exec \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-html_review_style pythonic \
-execute

The output of my afni_proc.py script with errors:
[Yashs-Air:~] yashkommula% afni_proc.py \
-subj_id AES101_Exercise \
-copy_anat Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatSS.AES101.nii \
-anat_has_skull no \
-anat_follower anat_w_skull anat Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXanat_shft.nii.gz \
-dsets Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXpicviewing_shft.nii.gz \
-blocks tshift align tlrc volreg blur mask scale regress \
-radial_correlate_blocks tcat volreg \
-tcat_remove_first_trs 2 \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.nii \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.aff12.1D \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_epi_anat yes \
? -subj_id AES101_Exercise \
? -copy_anat Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatSS.AES101.nii \
? -anat_has_skull no \
? -anat_follower anat_w_skull anat Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXanat_shft.nii.gz \
? -dsets Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXpicviewing_shft.nii.gz \
? -blocks tshift align tlrc volreg blur mask scale regress \
? -radial_correlate_blocks tcat volreg \
? -tcat_remove_first_trs 2 \
? -align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
? -tlrc_base MNI152_2009_template_SSW.nii.gz \
? -tlrc_NL_warp \
? -tlrc_NL_warped_dsets Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.nii \
? Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.aff12.1D \
? Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101_WARP.nii \
? -volreg_align_to MIN_OUTLIER \
? -volreg_align_e2a \
? -volreg_tlrc_warp \
? -mask_epi_anat yes \
? -blur_size 4.0 \
-regress_stim_times Volumes/E4BHData/stimtimes/neutral.1D Volumes/E4BHData/stimtimes/pleasant.1D Volumes/E4BHData/stimtimes/unpleasant.1D \
-regress_stim_labels neutral pleasant unpleasant \
-regress_basis 'BLOCK(20,1)' \
-regress_opts_3dD \
-jobs 4 \
-gltsym 'SYM: pleasant -neutral' \
-glt_label 1 P-N \
-gltsym 'SYM: unpleasant -neutral' \
-glt_label 2 U-N \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.05 \
-regress_3dD_stop \
-regress_reml_exec \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-html_review_style pythonic \
-execute? -regress_stim_times Volumes/E4BHData/stimtimes/neutral.1D Volumes/E4BHData/stimtimes/pleasant.1D Volumes/E4BHData/stimtimes/unpleasant.1D \
? -regress_stim_labels neutral pleasant unpleasant \
? -regress_basis 'BLOCK(20,1)' \
? -regress_opts_3dD \
? -jobs 4 \
? -gltsym 'SYM: pleasant -neutral' \
? -glt_label 1 P-N \
** missing run 1 dataset: Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXpicviewing_shft.nii.gz
----------------------------------------------------------------------
** failed command (create_blocks):

afni_proc.py -subj_id AES101_Exercise -copy_anat \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatSS.AES101.nii \
-anat_has_skull no -anat_follower anat_w_skull anat \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXanat_shft.nii.gz \
-dsets \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXpicviewing_shft.nii.gz \
-blocks tshift align tlrc volreg blur mask scale regress \
-radial_correlate_blocks tcat volreg -tcat_remove_first_trs 2 \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip -tlrc_base \
MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.nii \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101.aff12.1D \
Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/anatQQ.AES101_WARP.nii \
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp \
-mask_epi_anat yes -blur_size 4.0 -regress_stim_times \
Volumes/E4BHData/stimtimes/neutral.1D \
Volumes/E4BHData/stimtimes/pleasant.1D \
Volumes/E4BHData/stimtimes/unpleasant.1D -regress_stim_labels neutral \
pleasant unpleasant -regress_basis 'BLOCK(20,1)' -regress_opts_3dD \
-jobs 4 -gltsym 'SYM: pleasant -neutral' -glt_label 1 P-N ' '
----------------------------------------------------------------------
[Yashs-Air:~] yashkommula% -gltsym 'SYM: unpleasant -neutral' \
-gltsym: Command not found.
[Yashs-Air:~] yashkommula% -glt_label 2 U-N \
-glt_label: Command not found.
[Yashs-Air:~] yashkommula% -regress_motion_per_run \
? -regress_censor_motion 0.3 \
? -regress_censor_outliers 0.05 \
? -regress_3dD_stop \
? -regress_reml_exec \
? -regress_compute_fitts \
? -regress_make_ideal_sum sum_ideal.1D \
? -regress_est_blur_epits \
? -regress_est_blur_errts \
? -regress_run_clustsim no \
? -html_review_style pythonic \
? -execute
-regress_motion_per_run: Command not found.


Thank you,
Yash
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Subject Author Posted

errors running afni_proc.py

yk40_ June 09, 2021 04:37PM

Re: errors running afni_proc.py

ptaylor June 09, 2021 05:17PM

Re: errors running afni_proc.py

yk40_ June 10, 2021 08:04AM

Re: errors running afni_proc.py

ptaylor June 10, 2021 06:41PM

Re: errors running afni_proc.py

yk40_ June 24, 2021 02:13PM