multiparametric-fixed-fov

Processing pipeline (multi-subjects) for processing multi-parametric data when FOV is systematically centered at a particular disc or mid-vertebral level. This prior knowledge enables us to bypass the registration between the template and an anatomical data (typically T1 or T2), from which we can get the vertebral level information.

This pipeline will loop across all subjects (or only the subjects that you have specified) located under the data folder and results will be concatenated into single csv files where each row will correspond to a subject. The files will be output in the data folder.

The following metric is output:

• mt: MTR in WM in whole WM and sub-tracts, averaged across slices

In future versions of this pipeline, the following example metrics will be added:

• dmri: FA, MD, etc. in whole WM and sub-tracts, averaged across slices
• mt: MTsat in whole WM and sub-tracts, averaged across slices

Dependencies

This pipeline was tested on SCT v3.2.4. This pipeline also relies on FSLeyes for active quality control (QC).

File structure

data
  |- 001
  |- 002
  |- 003
      |- mt
        |- mt1.nii.gz
        |- mt0.nii.gz
        |- t1w.nii.gz

How to run

• Organize your data as indicated above
• Download (or git clone) this repository.
• Go to the repository folder: cd multiparametric-fixed-fov
• Copy the file parameters_template.sh and rename it as parameters.sh.
• Edit the file parameters.sh and modify the variables according to your needs:
  • PATH_DATA: Absolute path to the DATA folder. E.g.: /Users/bob/data
  • SUBJECTS: List of subjects to analyze. If you want to analyze all subjects in the PATH_DATA folder, then comment this variable.
  • METRICS_VERT_LEVEL: Vertebral levels to compute MRI metrics from. For example, if you want to extract metrics from levels 2, 3, 4 and 5, set this variable as METRICS_VERT_LEVEL="2,3,4,5".
  • PATH_RESULTS: Path where results will be stored. Default is: $PATH_DATA/results
  • Superior-Inferior (S-I) location of the center of FOV: Uncomment only one of the following variables, depending if the FOV is centered at a disc or at a mid-vertebral level, and replace X with the value corresponding to your acquisition setup. For example, if the MRI volume is centered at the mid-T10 vertebral level, then uncomment MIDFOV_VERT and set the value to 17 (see figure below):
    • MIDFOV_DISC=X
    • MIDFOV_VERT=X:

• Once the file parameters.sh is configured, you can run the pipeline as follows:
  • Process data: Will do most of the processing. A QC folder will be generated to check template registration.

./run_process.sh 1_process_data.sh

• Compute metrics: Extract metrics within specified labels and levels.

./run_process.sh 2_extract_metrics.sh

Contributors

Julien Cohen-Adad