afni_preprocess_before_signal_change_faces.py

# code to preprocess afni data before faces
import os
import glob
from shutil import copyfile
import pandas as pd
import json
import numpy as np


fmriprep_out="/data/jux/cnds/amennen/rtAttenPenn/fmridata/Nifti/derivatives/fmriprep"
task_path = '/data/jux/cnds/amennen/rtAttenPenn/fmridata/behavdata/faces'
run_path = '/data/jux/cnds/amennen/rtAttenPenn/fmridata/Nifti/derivatives/afni/first_level/normalized_runs'
cf_dir = '/data/jux/cnds/amennen/rtAttenPenn/fmridata/Nifti/derivatives/fsl/first_level/confound_EVs'
timing_path = '/data/jux/cnds/amennen/rtAttenPenn/fmridata/Nifti/derivatives/afni/first_level/timing_files'
analyses_out = '/data/jux/cnds/amennen/rtAttenPenn/fmridata/Nifti/derivatives/afni/first_level/stats'
whole_brain_mask = '/data/jux/cnds/amennen/rtAttenPenn/MNI_things/mni_icbm152_t1_tal_nlin_asym_09c_BOLD_mask_Penn.nii'
subjectNum = np.int(sys.argv[1])
bids_id = 'sub-{0:03d}'.format(subjectNum)
all_categories = ['fearful','happy', 'neutral', 'object']