dipy_fit_dsid#

Synopsis#

Diffusion Spectrum Imaging (DSI) reconstruction workflow.

In DSI, the diffusion signal is sampled on a Cartesian grid in q-space. When using remove_convolution=True, the convolution on the DSI propagator that is caused by the truncation of the q-space in the DSI sampling is removed.

Usage#

dipy_fit_dsid [OPTIONS] input_files bvalues_files bvectors_files mask_files

Input Parameters#

  • input_files

    Path to the input volumes. This path may contain wildcards to process multiple inputs at once.

  • bvalues_files

    Path to the bvalues files. This path may contain wildcards to use multiple bvalues files at once.

  • bvectors_files

    Path to the bvectors files. This path may contain wildcards to use multiple bvectors files at once.

  • mask_files

    Path to the input masks. This path may contain wildcards to use multiple masks at once.

General Options#

  • --qgrid_size

    has to be an odd number. Sets the size of the q_space grid. For example if qgrid_size is 17 then the shape of the grid will be (17, 17, 17). (default: 17)

  • --r_start

    ODF is sampled radially in the PDF. This parameters shows where the sampling should start. (default: 2.1)

  • --r_end

    Radial endpoint of ODF sampling (default: 6.0)

  • --r_step

    Step size of the ODf sampling from r_start to r_end (default: 0.2)

  • --filter_width

    Strength of the hanning filter (default: 32)

  • --remove_convolution

    Whether to remove the convolution on the DSI propagator that is caused by the truncation of the q-space in the DSI sampling. (default: False)

  • --normalize_peaks

    Whether to normalize the peaks (default: False)

  • --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)

  • --sh_order_max

    Spherical harmonics order (l) used in the DKI fit. (default: 8)

  • --extract_pam_values

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

  • --parallel

    Whether to use parallelization in peak-finding during the calibration procedure. (default: False)

  • --num_processes

    If parallel is True, the number of subprocesses to use (default multiprocessing.cpu_count()). If < 0 the maximal number of cores minus num_processes + 1 is used (enter -1 to use as many cores as possible). 0 raises an error. (default: None)

Output Options#

  • --out_dir

    Output directory. (default: current directory)

  • --out_pam

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

  • --out_shm

    Name of the spherical harmonics volume to be saved. (default: shm.nii.gz)

  • --out_peaks_dir

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

  • --out_peaks_values

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

  • --out_peaks_indices

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

  • --out_gfa

    Name of the generalized FA volume to be saved. (default: gfa.nii.gz)

  • --out_sphere

    Sphere vertices name to be saved. (default: sphere.txt)

  • --out_b

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

  • --out_qa

    Name of the Quantitative Anisotropy to be saved. (default: qa.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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