dipy_fit_mapmri#

Synopsis#

Workflow for fitting the MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng saved in a nifti format in input files provided by data_files and saves the nifti files to an output directory specified by out_dir.

In order for the MAPMRI workflow to work in the way intended either the Laplacian or positivity or both must be set to True.

Usage#

dipy_fit_mapmri [OPTIONS] data_files bvals_files bvecs_files small_delta big_delta

Input Parameters#

  • data_files

    Path to the input volume.

  • bvals_files

    Path to the bval files.

  • bvecs_files

    Path to the bvec files.

  • small_delta

    Small delta value used in generation of gradient table of provided bval and bvec.

  • big_delta

    Big delta value used in generation of gradient table of provided bval and bvec.

General Options#

  • --b0_threshold

    Threshold used to find b0 volumes. (default: 50.0)

  • --laplacian

    Regularize using the Laplacian of the MAP-MRI basis. (default: True)

  • --positivity

    Constrain the propagator to be positive. (default: True)

  • --bval_threshold

    Sets the b-value threshold to be used in the scale factor estimation. In order for the estimated non-Gaussianity to have meaning this value should set to a lower value (b<2000 s/mm^2) such that the scale factors are estimated on signal points that reasonably represent the spins at Gaussian diffusion. (default: 2000)

  • --save_metrics

    List of metrics to save. Possible values: rtop, laplacian_signal, msd, qiv, rtap, rtpp, ng, perng, parng (default: ())

  • --laplacian_weighting

    Weighting value used in fitting the MAPMRI model in the Laplacian and both model types. (default: 0.05)

  • --radial_order

    Even value used to set the order of the basis. (default: 6)

  • --sphere_name

    Sphere name on which to reconstruct the fODFs. (default: None)

  • --relative_peak_threshold

    Only return peaks greater than relative_peak_threshold * m where m is the largest peak. (default: 0.5)

  • --min_separation_angle

    The minimum distance between directions. If two peaks are too close only the larger of the two is returned. (default: 25)

  • --npeaks

    Maximum number of peaks found. (default: 5)

  • --normalize_peaks

    If true, all peak values are calculated relative to max(odf). (default: False)

  • --extract_pam_values

    Save or not to save pam volumes as single nifti files. (default: False)

Output Options#

  • --out_dir

    Output directory. (default: current directory)

  • --out_rtop

    Name of the rtop to be saved. (default: rtop.nii.gz)

  • --out_lapnorm

    Name of the norm of Laplacian signal to be saved. (default: lapnorm.nii.gz)

  • --out_msd

    Name of the msd to be saved. (default: msd.nii.gz)

  • --out_qiv

    Name of the qiv to be saved. (default: qiv.nii.gz)

  • --out_rtap

    Name of the rtap to be saved. (default: rtap.nii.gz)

  • --out_rtpp

    Name of the rtpp to be saved. (default: rtpp.nii.gz)

  • --out_ng

    Name of the Non-Gaussianity to be saved. (default: ng.nii.gz)

  • --out_perng

    Name of the Non-Gaussianity perpendicular to be saved. (default: perng.nii.gz)

  • --out_parng

    Name of the Non-Gaussianity parallel to be saved. (default: parng.nii.gz)

  • --out_pam

    Name of the peaks volume to be saved. (default: mapmri_peaks.pam5)

  • --out_peaks_dir

    Name of the peaks directions volume to be saved. (default: mapmri_peaks_dirs.nii.gz)

  • --out_peaks_values

    Name of the peaks values volume to be saved. (default: mapmri_peaks_values.nii.gz)

  • --out_peaks_indices

    Name of the peaks indices volume to be saved. (default: mapmri_peaks_indices.nii.gz)

References#

Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.

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