cubric-physio

Physiological Noise Correction using the PhysIO Toolbox - Examples for CUBRIC, Cardiff

Purpose

This small repository sets up a simple preprocessing (realignment)

Installation

1. You will need to install SPM12
2. You will need to install the PhysIO Toolbox
   • The PhysIO/code folder should end up in spm12/toolbox/PhysIO

Getting Started

1. Open the main script cubric_main in Matlab
2. Follow the instructions there to adapt paths to your environment
3. For each subject to try, copy the fMRI and physiological recording data according to the following naming conventions into a new folder results/sub-XX (XX is subject ID, e.g., 15)
   • *3DT1*.nii -> results/sub-XX/nifti/struct.nii
   • *rFMRI*.nii -> results/sub-XX/nifti/fmri.nii
     • Note that this only assesses the resting state run for now. You can number the runs fmri1.nii, fmri2.nii etc., but you will have to adapt all job files *_spm_job.m in the code to reflect the right file names.
   • LabChart*.txt -> SCANPHYSLOG.log
     • Note that you have to choose the log file where the <TimeStamp>
       roughly matches (being a bit earlier, but < 1 min) the AcquisitionTime in the .json sidecar file of the corresponding *rFMRI*.nii file
4. Run cubric_physio_main (play button) in Matlab. For starters, the interactive mode (isInteraxtive = true) is recommended