MTsat: Magnetization transfer saturation¶

Usage¶

nextflow run mtsatflow_BIDS.nf [OPTIONAL_ARGUMENTS] (--root)

Description¶

--root=/path/to/[root] Root folder containing multiple subjects

Container requirements¶

If you have Docker installed, enabling docker option will make use of the following Docker images to execute processes:

Local installation requirements¶

Unless the docker option is enabled in the nextflow.config, the following dependencies must be installed and added to the system path:

Folder organization¶

https://upload.wikimedia.org/wikipedia/commons/d/de/BIDS_Logo.png
[root]
├── sub-01
│   │── anat
│   │   ├── sub-01_acq-MTon_MTS.nii.gz
|   |   ├── sub-01_acq-MTon_MTS.json
│   │   ├── sub-01_acq-MToff_MTS.nii.gz
│   │   ├── sub-01_acq-MToff_MTS.json
│   │   ├── sub-01_acq-T1w_MTS.nii.gz
│   │   └── sub-01_acq-T1w_MTS.json
│   └── fmap
│       └── sub-01_B1plusmap.nii.gz (optional)
└── sub-02
    │── anat
    │   ├── sub-02_acq-MTon_MTS.nii.gz
    |   ├── sub-02_acq-MTon_MTS.json
    │   ├── sub-02_acq-MToff_MTS.nii.gz
    │   ├── sub-02_acq-MToff_MTS.json
    │   ├── sub-02_acq-T1w_MTS.nii.gz
    │   └── sub-02_acq-T1w_MTS.json
    └── fmap
        └── sub-02_B1plusmap.nii.gz (optional)

Optional arguments¶

--platform ["octave"/"matlab"] Platform choice.
--qmrlab_dir ["/path/to/qMRLab" OR null] Absolute path to the qMRLab’s
root directory. If docker is enabled, MUST be set
to null (without double quotes). If docker is NOT enabled,
then the absolute path to the qMRLab MUST be provided.
Note that qMRLab version MUST be equal or greater than v2.3.1.
--octave_path ["/path/to/octave_exec" OR null] Absolute path to Octave’s
executable. If docker is enabled, or, if you’d like to use
Octave executable saved to your system path, MUST be set to
null (without double quotes).
--matlab_path ["/path/to/matlab_exec" OR null] Absolute path to MATLAB’s
executable. If you’d like to use MATLAB executable saved to
your system path, MUST be set to null (without double quotes).
Note that qMRLab requires MATLAB > R2014b. Docker image
containing MCR compiled version of this application is NOT
available yet. Therefore, container declarations for the
processes starting with Fit prefix MUST be set to null
(without double quotes).
--ants_dim [2/3/4] This option forces the image to be treated
as a specified-dimensional image. If not specified,
ANTs tries to infer the dimensionality.
--ants_metric ["MI"] Confined to MI: Mutual information, for this
particular pipeline.
--ants_metric_weight
 [0-1] If multimodal (i.e. changing contrast) use weight 1.
This parameter is used to modulate the per stage weighting
of the metrics.
--ants_metric_bins
 [e.g. 32] Number of bins.
--ants_metric_sampling
 ["Regular","Random:] The point set can be on a regular
lattice or a random lattice of points slightly perturbed
to minimize aliasing artifacts.
--ants_metric_samplingprct
 [0-100] The fraction of points to select from the domain
--ants_transform
 
  • "Rigid"
  • "Affine"
  • "CompositeAffine"
  • "Similarity"
  • "Translation"
  • "BSpline"
--ants_convergence
 [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]
Convergence is determined from the number of iterations per level
and is determined by fitting a line to the normalized energy
profile of the last N iterations (where N is specified by the window
size) and determining the slope which is then compared with
the convergence threshold.
--ants_shrink [MxNxO] Specify the shrink factor for the virtual domain (typically
the fixed image) at each level.
--ants_smoothing
 [MxNxO] Specify the sigma of gaussian smoothing at each level.
Units are given in terms of voxels (‘vox’) or physical spacing (‘mm’).
Example usage is ‘4x2x1mm’ and ‘4x2x1vox’ where no units implies
voxel spacing.
--use_b1cor [true/false] Use and RF transmit field to correct for flip angle
imperfections.
--b1cor_factor [0-1] Correction factor (empirical) for the transmit RF. Only
corrects MTSAT, not T1. Default 0.4.
--use_bet Use FSL’s BET for skull stripping.
--bet_recursive
 [true/false] This option runs more “robust” brain center estimation.
--bet_threshold
 [0-1] Fractional intensity threshold (0->1); default=0.45;
smaller values give larger brain outline estimates.

Notes¶

  • BIDS for quantitative MRI (BEP001) data is under development as of early 2020. You can visit the BEP001 GitHub repository.

  • Example datasets:

  • Files should be compressed Nifti files (.nii.gz)

  • Timing parameters in the .json files MUST be in seconds.

  • Subject IDs are used as the primary process ID and tag throughout the pipeline.

  • We adhere to a strict one-process one-container mapping, where possible using off-the shelf qMRLab containers.

  • All the OPTIONAL ARGUMENTS can be modified in the nextflow.config file. The same config file is consumed by mtrflow_BIDS.nf.

  • You can take advantage of Nextflow’s comprehensive tracing and visualization features while executing this pipeline: https://www.nextflow.io/docs/latest/tracing.html.

  • For any requests, questions or contributions, please feel free to open an issue at qMRflow’s GitHub repo at https://github.com/qMRLab/qMRflow.

Reference¶

Please cite the following if you use this module:

Karakuzu A. et al. 2019 The qMRLab workflow: From acquisition to publication., ISMRM 27th Annual Meeting and Exhibition, Montreal, Canada.