1_head_motion

Calculate head motion from BOLD data during task runs

Note: These scripts were run on the Habanero HPC at Columbia University

1_submit_moco_haba.sh

This is a slurm launch script for running motion correction for one scan run. This script will be run many times in parallel by 2_haba_bold_motion_assess_all_emotions.py.

1. The script takes 2-command line arguments for curDir (the current directory where the BOLD file is saved) and boldFile (the BOLD file to be assessed for motion)
2. For the given BOLD file, run fsl_motion_outliers to generate an estimate of framewise displacement for each TR, as well as a 1-column file denoting TRs where FD > 0.9mm (we chose a threshold of .9mm). This file will later be used to downweight these high-motion TRs in the GLM

This file, called confound.txt will have k column and 130 rows (1 row per TR, where k is the number of TRs over the given threshold). For example, if the below were the first 5 rows of the file with k=2, this would indicate that in the 3rd volume and 4th volumes there were spikes in framewise displacement (FD) above our threshold of .9mm. Later, we'll downweight these volume in the GLM so that BOLD signal specifically during this volume doesn't influence estimates of task-evoked reactivity or functional connectivity. Each column will be one regressor in the GLM, effectively making sure that no other regressors will be able to account for the variance in the row marked by the 1

0   0
0   0
1   0
0   1
0   0

This also creates a file called outlier_output.txt with some useful info on how many total outliers of the chosen metric (framewise displacement) were detected.

ndel = 0 ; mask =  ; do_moco = yes ; thresh = .9 ; use_thresh = yes ; metric = fd
brainmed = 714.000000  ; maskmean = 0.345725 
Calculating outliers
Range of metric values: 0.012444 1.400310 
Found 1 outliers over .9
Generating EVs
Found spikes at  128

2_haba_bold_motion_assess_all_emotions.py

Loops through all BOLD files available, then launches 1_submit_moco_haba.sh to run in parallel for all of them.