Hi I'm still struggling with this section, I'm getting an error specific to the 3dDeconvolve section (that I'm pasting below)
I created my txt files in the attached document (I just have one run and random timing - at the moment to debug my script )

This is the error I'm getting (I looked for this error on this board, one person has solved it by adding stim_times_AM1 but it's in my script (see below) and does not help.

looks like I fix the error on 3Ddeconvolve, now I need to adjust it in my AFNI proc.py script

3dDeconvolve -input ${analysisdir}/pb03.$subj.r*.blur+orig.HEAD \
-ortvec ${analysisdir}/mot_demean.r01.1D mot_demean_r01 \
-polort 3 \
-num_stimts 2 \
-stim_times_AM1 1 ${analysisdir}/stimuli/offset_congruent.stimtimes.txt 'dmBLOCK(1)' \
-stim_label 1 Congruent \
-stim_times_AM1 2 ${analysisdir}/stimuli/offset_incongruent.txt 'dmBLOCK(1)' \
-stim_label 2 Incongruent \
-jobs 16 \
-gltsym 'SYM: +Incongruent -Congruent' \
-glt_label 1 'Incongruent vs Congruent' \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.${subj} \
-x1D_stop \
-bucket stats.$subj


ALSO placing my afniproc py script below

#!/bin/bash
#Name: Targeting.sh
# Author: LB
# Date: 7/12/22
# Syntax: ./Targeting.sh SUBJ
# Arguments: SUBJ: subject ID
# Description: This script will run all chosen scans through the afni_proc.py pipeline
# Requirements: 1) AFNI
# Notes: --

if [ "$#" -eq 1 ]; then
subj=$1
else
echo "Specify participant ID Please"
exit 1
fi


pwd_dir=`pwd`
proj_dir=${pwd_dir%/*}

## SETTING UP THE DIRECTORIES
anatdir=${proj_dir}/Anat/${subj}
funcdir=${proj_dir}/Func/${subj}
stimdir=${proj_dir}/Behav/${subj}
analysisdir=${proj_dir}/Analysis/${subj}
cd ${analysisdir}

## DATA CHECK
#for anat
if [ -f "${anatdir}/${subj}_T1.nii" ] ; then
echo -e "\033[0;35m++ Found T1 of $subj... ++\033[0m"
else
echo -e "\033[0;35m++ This participant does not have T1 scan .. EXITING ++\033[0m"
exit
fi

if [ -f "${funcdir}/${subj}_Stroop_Run01.nii" ] ; then
echo -e "\033[0;35m++ Found functional for participant ${subj}, moving to next step ... ++\033[0m"
else
echo -e "\033[0;35m++ Subject $subj does not have functional scans... EXITING ++\033[0m"
exit 1
fi


## SETTING UP AFNI ## need to add fixation and ITI and incorrect as stim

afni_proc.py \
-subj_id ${subj} \
-blocks tshift align volreg blur mask regress \
-copy_anat ${anatdir}/${subj}_T1.nii \
-dsets \
${funcdir}/${subj}_Stroop_Run01.nii \
-tcat_remove_first_trs 5 \
-regress_stim_times_offset -10 \
-align_opts_aea -cost lpc+ZZ -giant_move \
-anat_uniform_method unifize \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-regress_est_blur_errts \
-blur_size 4.0 \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_reml_exec \
-regress_3dD_stop \
-regress_stim_types AM1 \
-regress_stim_times \
${stimdir}/congruent.stimtimes.txt \
${stimdir}/incongruent.txt \
-regress_stim_labels Congruent Incongruent \
-regress_basis 'dmBLOCK(1)' \
-regress_opts_3dD -jobs 16 \
-gltsym 'SYM: Incongruent-Congruent' \
-glt_label Incongruent - Congruent\
-outdir ${analysisdir} \
-html_review_style pythonic \
-execute


Do you know what I'm doing wrong? Thank you very much in advance



Edited 3 time(s). Last edit at 07/13/2022 11:04AM by Lysianne.