dipy_fit_dsi#
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_dsi [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.