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Processing Physiological Files



Convert AcqKnowledge BioPac files to BIDS Physiologicals (.tsv.gz/.json)) & trim to functional length


Download acq2bidsphysio from GitHub (locally or on Biowulf)

git clone https://github.com/cbinyu/bidsphysio.git


Convert the .acq files to BIDS format (BIDSPhysio) with Physio_Proc.sh. This call will extract the acquisition times from 1st echo functionals, which you can use to enter the corresponding date and time of acquisition for the .acq files. Enter 'module load jq' first.
Note: This step is very manual, and detail- and time-intensive, so should be done after every scan.

bash Physio_Proc.sh sub-?? convert
Enter task run:
wnw 1
Enter date:
2022-01-01T09_00_00


Trim the physiological files with Physio_Proc.sh and enter 'trim' at the 'process to call' prompt. The trimmed files will be dropped in the 'Unprocessed/func/' directory.

bash Physio_Proc.sh sub-?? trim


Note: you can trim for multiple subjects with the following command:

for s in sub-{01..25}; do bash Physio_Proc.sh $s trim; done


Calculate physiological regressors via NiPhlem


This call will calculate the design matrix of NiPhlem and AFNI physiological regressors and will drop them in each subject-level directory called 'sub-??/Regressors/'.

bash Physio_Proc.sh sub-?? calc_regressors 
OR
for s in sub-{01..25}; do bash Physio_Proc.sh $s calc_regressors; done


Fit the ICA components to the regressors with a Linear Model


Call run_FitReg2ICA.sh

bash run_FitReg2ICA.sh

This file will run FitReg2ICA.py, which runs on a group of subjects listed in the file.
To see the methods used in the FitReg2ICA class obj, view FitReg2ICAClass.py.


Optional: plot the regressors to view them


This call will enable you to view the plots of your Niphlem and AFNI regressors that you are including in your design matrix. These plots include: peak-detection, motion parameter plots (first derivative and demeaned), Retroicor, HRV/RVT plots, and WM/CSF plots. All of these plots are time-series.

bash Physio_Proc.sh sub-?? plot_regressors
OR
for s in sub-{01..25}; do bash Physio_Proc.sh $s plot_regressors; done