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March 08, 2021 05:15PM
Hello afni experts,

I have to run my afni pipeline in two steps as I want to take the data after preprocessing and run wavelet despiking on it, and bring it then back to afni to run the regress block (for nuisance regression for resting state analysis). My problem is that for some reasons 3dDeconvolve does not calculate the demean and derivative from the motion regressors. What am I missing in my command? Maybe I need to run 1d_tool.p and calculate the -demean and -derivative before 3dDeconvolve?
(The directory where I run this command includes the despiked dataset, and the dfile_rall.1D file)

I am using the following afni_proc.py command for the regression

afni_proc.py -subj_id ${subj}\
-script proc.py_scripts2/proc_${subj}.sh\
-out_dir ${top_dir}${subj}/${subj}.3dDeconvolve\
-dsets ${func_dir}pb04.P1002.scale_masked_Despiked_wds.nii.gz\
-blocks regress\
-regress_apply_mot_types demean deriv\
-regress_extra_ortvec ${stim_times_dir}cwm.1D ${stim_times_dir}ccsf.1D\
-regress_extra_ortvec_labels cwm ccsf
Subject Author Posted

running only regress block with -regress_apply_mot_types demean deriv

carolin31 March 08, 2021 05:15PM

Re: running only regress block with -regress_apply_mot_types demean deriv

Peter Molfese March 09, 2021 11:37AM

Re: running only regress block with -regress_apply_mot_types demean deriv

rick reynolds March 09, 2021 11:49AM

Re: running only regress block with -regress_apply_mot_types demean deriv

carolin31 March 09, 2021 08:40PM



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