Multiband Artifact Regression in Simultaneous Slices (MARSS)

Detection and removal of an artifactual shared signal between simultaneously acquired slices in unprocessed multiband fMRI.

MARSS

Multiband Artifact Regression in Simultaneous Slices (MARSS)

This is a MATLAB pipeline developed for use in simultaneous multi-slice (multiband; MB) fMRI data. MARSS is a regression-based method that mitigates an artifactual shared signal between simultaneously acquired slices in unprocessed MB fMRI.

Software Authors: Philip Tubiolo, John C. Williams, Mahika Gupta, and Jared X. Van Snellenberg

Software Requirements

This software uses SPM12, which is included in this distribution. For more information, visit https://www.fil.ion.ucl.ac.uk/spm/software/spm12/ .
This software was developed on MATLAB R2023b and has been tested for compatibility on MATLAB R2021a.
This software has been tested on the following operating systems, but should be compatible with MacOS as well:
Linux: Red Hat Enterprise Linux 7.9
Windows: Windows 10 Home 64-bit

Hardware Requirements

MARSS should only require the minimum RAM to handle a single fMRI timeseries (approximately 2GB). However, it has been tested with these minimum specifications:
RAM: 16 GB
Processor: Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz

With the above specifications, the total time taken for MARSS to complete on a single fMRI timeseries of 563 volumes is approximately 10 minutes.

Usage

MARSS.m

MARSS.m is the main function of this pipeline, and the only function that must be directly run in order to perform MARSS on a single timeseries.

Syntax

MARSS(timeseriesFile, MB, workingDir) performs MARSS artifact correction on a single unprocessed, MB fMRI timeseries.

Input Arguments

timeseriesFile (string): Full path to unprocessed, MB fMRI timeseries
MB (double): Multiband Acceleration Factor used during image acquisition
workingDir (string): Parent directory for all MARSS outputs. MARSS will create a separate folder within this folder named after timeseriesFile.

Outputs in workingDir

MARSS_SliceCorrelations.mat: this .mat file contains a structure array with slice correlation information in pre- and post-MARSS data. This includes the slice correlation matrices, average correlation between simultaneously acquired slices, and average correlation between adjacent slices.
za_.nii: this NIFTI is the MARSS corrected timeseries.
_slcart.nii: this NIFTI is the timeseries of MARSS-estimated artifact signal that was subtracted from timeseriesFile to produce za*.nii
_AVGslcart.nii: this NIFTI is the average across timepoints of slcart.nii (shown as a single 3D volume).
MARSS_.png: this is a summary diagnostic figure depicting pre- and post-MARSS slice correlation matrices, as well as orthogonal views of the artifact spatial distribution (from _AVGslcart.nii).

Citation

When using MARSS, please cite the following: Insert paper here

License

This software is released under the GNU General Public License Version 3.