Image analysis pipelines of qunatitative MRI (qMRI), including diffusion MRI (dMRI), in patients with adrenoleukodystrophy (ALD)
- Introduction
- DICOM to NIfTI conversion
- MRI info check
- Automated pipelines
- DTI analysis
- References
- Copyright
ANYONE CAN CONTRIBUTE to the open-source MATLAB/Octave software library for automated image and statistical analyses. The library includes:
- DTI analysis of longitudinal 12-directional diffusion MRI data
(Pierpont and Labounek, et al. 2024)
The script bin/ald_convert_data.sh demonstrates how a multi-center MRI data were converted from DICOM format into NIfTI format and stored in a unified folder and file naming structure.
The script bin/ald_datacheck.sh can further check whether specific MRI image is or is not abvailable over list of subjects and particular MRI sessions.
The script bin/ald_mri_info.sh can read MRI image info such as voxel dimensions and voxel volume over list of subjects and particular MRI sessions.
The bash script bin/ald_pipeline.sh proceed the entire image analysis. The pipeline provides:
- MPRAGE image analysis
- DTI analysis
- T1-rho / T2-rho image analysis
The bash script bin/ald_dmri_process.sh proceed automated preprocessing and DTI analysis of longitudinal 12-directional diffusion MRI data for the protocol optimized and presented in (Pierpont and Labounek, et al. 2024).
After DTI analysis is done, the matlab script matlab/ald_extract_dmri_metrics.m can extract local microstructural measurements from DTI results.
When all results are organized in excel sheet like in the data/data_pierpont_labounek_2024.xlsx file, then the matlab script matlab/ald_evaluation.m can provide statistical analysis and make figures including graphs and tables as presented in (Pierpont and Labounek, et al. 2024).
Pierpont E I, Labounek R, Gupta A O, Lund T C, Orchard P J, Dobyns W B, Bondy M, Paulson A, Metz A, Shanley R, Wozniak J R, Mueller B A, Loes D, Nascene D R, & Nestrasil I (2024). Diffusion tensor imaging is sensitive to early demyelinating lesions and predicts neurocognitive outcome in boys with adrenoleukodystrophy. [Under review]
The "qmri-ald" program provides automated image-processing pipelines for structural MRI images primarily acquired in pediatric healthy controls and pediatric patients with cerebral adrenoleukodystrophy. The program provides preprocessing, processing, quantitative, and statistical analysis of MRI images such as T1-weighted anatomical scans, diffusion MRI scans utilizing DTI and HARDI protocols or T1-rho and T2-rho scans.
Copyright (C) 2024 Rene Labounek (1,a), Igor Nestrasil (1,b), Medical Imaging Lab (MILab)
1 Medical Imaging Lab (MILab), Division of Clinical Behavioral Neuroscience, Department of Pediatrics, University of Minnesota, Masonic Institute for the Developing Brain, 2025 East River Parkway, Minneapolis, MN 55414, USA
a) email: rlaboune@umn.edu
b) email: nestr007@umn.edu
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.