-x1D_stop is automatically invoked by afni_proc.py

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Hi everyone,

I am running afni_proc.py and finding that -x1D_stop is being automatically included in the 3dDeconvolve command triggered by the regress block. I am not sure why or how to remove it from the afni_proc.py level, but needless to say it is stopping the processing pipeline.

-motion files and glm look normal
-no other warnings above, except regress/blur maybe are flipped?

Thanks for any pointers!
Laurel

python afni_proc.py -dsets  generic/1scans_17.nii generic/scans_23.nii generic/scans_25.nii  -blur_size 5 -blocks despike tshift align tlrc volreg mask regress blur -regress_apply_mot_types demean deriv -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim yes -volreg_align_e2a -copy_anat aseg_mask_uni.nii.gz -anat_has_skull no

#copied from *.out file:
3dDeconvolve -input pb03.SUBJ.r01.volreg+orig.HEAD pb03.SUBJ.r02.volreg+orig.HEAD pb03.SUBJ.r03.volreg+orig.HEAD -polort 3 -num_stimts 12 -stim_file 1 motion_demean.1D[0] -stim_base 1 -stim_label 1 roll_01 -stim_file 2 motion_demean.1D[1] -stim_base 2 -stim_label 2 pitch_01 -stim_file 3 motion_demean.1D[2] -stim_base 3 -stim_label 3 yaw_01 -stim_file 4 motion_demean.1D[3] -stim_base 4 -stim_label 4 dS_01 -stim_file 5 motion_demean.1D[4] -stim_base 5 -stim_label 5 dL_01 -stim_file 6 motion_demean.1D[5] -stim_base 6 -stim_label 6 dP_01 -stim_file 7 motion_deriv.1D[0] -stim_base 7 -stim_label 7 roll_02 -stim_file 8 motion_deriv.1D[1] -stim_base 8 -stim_label 8 pitch_02 -stim_file 9 motion_deriv.1D[2] -stim_base 9 -stim_label 9 yaw_02 -stim_file 10 motion_deriv.1D[3] -stim_base 10 -stim_label 10 dS_02 -stim_file 11 motion_deriv.1D[4] -stim_base 11 -stim_label 11 dL_02 -stim_file 12 motion_deriv.1D[5] -stim_base 12 -stim_label 12 dP_02 -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -fitts fitts.SUBJ -errts errts.SUBJ -x1D_stop -bucket stats.SUBJ
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I would not expect that to be actually stopping the processing pipeline.

You are running as a resting state analysis, meaning there are no regressors of interest.

In that case, 3dDeconvolve is used merely to generate the regression matrix (of all noise). So indeed, it does terminate after -x1D_stop. But that is because the much faster 3dTproject program is then run to do the actual projection, since no regression statistics are needed.

The script should still continue after 3dDeconvolve, and you should still get the same errts output, just more quickly. It probably has tproject in the name, and the final QC text output should mention this.

  • rick
3

Thank you Rick- you are right!
Best,
Laurel