usage: __main__.py [-h] [--slice_index SLICE_INDEX] [--win_dims WIDTH HEIGHT]
[--interactor {trackball,image}]
[--axis_name {sagittal,coronal,axial}] [--silent]
[--in_transparency_mask IN_TRANSPARENCY_MASK]
[--output OUTPUT] [-f]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[--sphere {symmetric642,symmetric362,repulsion100,repulsion724,symmetric724,repulsion200}]
[--sph_subdivide SPH_SUBDIVIDE] [--mask MASK]
[--colormap COLORMAP | --color_rgb COLOR_RGB COLOR_RGB COLOR_RGB]
[--scale SCALE] [--radial_scale_off] [--norm_off]
[-v [{DEBUG,INFO,WARNING}]] [--background BACKGROUND]
[--bg_range MIN MAX] [--bg_opacity BG_OPACITY]
[--bg_offset BG_OFFSET]
[--bg_interpolation {linear,nearest}]
[--bg_color BG_COLOR BG_COLOR BG_COLOR] [--peaks PEAKS]
[--peaks_color PEAKS_COLOR PEAKS_COLOR PEAKS_COLOR]
[--peaks_width PEAKS_WIDTH]
[--peaks_values PEAKS_VALUES | --peaks_length PEAKS_LENGTH]
[--variance VARIANCE] [--variance_k VARIANCE_K]
[--var_color VAR_COLOR VAR_COLOR VAR_COLOR]
in_fodf
Visualize 2-dimensional fODF slice loaded from disk.
Given an image of SH coefficients, this script displays a slice in a
given orientation. The user can also add a background on top of which the
fODF are to be displayed. Using a full SH basis, the script can be used to
visualize asymmetric fODF. The user can supply a peaks image to visualize
peaks on top of fODF.
If a transparency_mask is given (e.g. a brain mask), all values outside the
mask non-zero values are set to full transparency in the saved scene.
!!! CAUTION !!! The script is memory intensive about (9kB of allocated RAM per
voxel, or 9GB for a 1M voxel volume) with a sphere interpolated to 362 points.
positional arguments:
in_fodf Input SH image file.
options:
-h, --help show this help message and exit
--slice_index SLICE_INDEX
Index of the slice to visualize along a given axis. Defaults to middle of volume.
--win_dims WIDTH HEIGHT
The dimensions for the vtk window. [(768, 768)]
--interactor {trackball,image}
Specify interactor mode for vtk window. [trackball]
--axis_name {sagittal,coronal,axial}
Name of the axis to visualize. [axial]
--silent Disable interactive visualization.
--in_transparency_mask IN_TRANSPARENCY_MASK
Input mask image file.
--output OUTPUT Path to output file.
-f Force overwriting of the output files.
--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}
Spherical harmonics basis used for the SH coefficients.
Must be either descoteaux07', 'tournier07',
'descoteaux07_legacy' or 'tournier07_legacy' [['descoteaux07_legacy']]:
'descoteaux07' : SH basis from the Descoteaux et al.
MRM 2007 paper
'tournier07' : SH basis from the new Tournier et al.
NeuroImage 2019 paper, as in MRtrix 3.
'descoteaux07_legacy': SH basis from the legacy Dipy implementation
of the Descoteaux et al. MRM 2007 paper
'tournier07_legacy' : SH basis from the legacy Tournier et al.
NeuroImage 2007 paper.
--sphere {symmetric642,symmetric362,repulsion100,repulsion724,symmetric724,repulsion200}
Name of the sphere used to reconstruct SF. [symmetric362]
--sph_subdivide SPH_SUBDIVIDE
Number of subdivisions for given sphere. If not supplied, use the given sphere as is.
--mask MASK Optional mask file. Only fODF inside the mask are displayed.
--colormap COLORMAP Colormap for the ODF slicer. If None, then a RGB colormap will be used. [None]
--color_rgb COLOR_RGB COLOR_RGB COLOR_RGB
Uniform color for the ODF slicer given as RGB, scaled between 0 and 1. [None]
--scale SCALE Scaling factor for FODF. [0.5]
--radial_scale_off Disable radial scale for ODF slicer.
--norm_off Disable normalization of ODF slicer.
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
Background arguments:
--background BACKGROUND
Background image file. If RGB, values must be between 0 and 255.
--bg_range MIN MAX The range of values mapped to range [0, 1] for background image. [(bg.min(), bg.max())]
--bg_opacity BG_OPACITY
The opacity of the background image. Opacity of 0.0 means transparent and 1.0 is completely visible. [1.0]
--bg_offset BG_OFFSET
The offset of the background image. [0.5]
--bg_interpolation {linear,nearest}
Interpolation mode for the background image. [nearest]
--bg_color BG_COLOR BG_COLOR BG_COLOR
The color of the overall background, behind everything. Must be RGB values scaled between 0 and 1. [(0, 0, 0)]
Peaks arguments:
--peaks PEAKS Peaks image file.
--peaks_color PEAKS_COLOR PEAKS_COLOR PEAKS_COLOR
Color used for peaks, as RGB values scaled between 0 and 1. If None, then a RGB colormap is used. [None]
--peaks_width PEAKS_WIDTH
Width of peaks segments. [1.0]
Peaks scaling arguments:
Choose between peaks values and arbitrary length.
--peaks_values PEAKS_VALUES
Peaks values file.
--peaks_length PEAKS_LENGTH
Length of the peaks segments. [0.65]
Variance arguments:
For the visualization of fodf uncertainty, the variance is used as follow: mean + k * sqrt(variance), where mean is the input fodf (in_fodf) and k is the scaling factor (variance_k).
--variance VARIANCE FODF variance file.
--variance_k VARIANCE_K
Scaling factor (k) for the computation of the fodf uncertainty. [1]
--var_color VAR_COLOR VAR_COLOR VAR_COLOR
Color of variance outline. Must be RGB values scaled between 0 and 1. [(1, 1, 1)]