.. _scil_viz_fodf: scil_viz_fodf ============= :: usage: __main__.py [-h] [--slice_index SLICE_INDEX] [--win_dims WIDTH HEIGHT] [--interactor {image,trackball}] [--axis_name {sagittal,coronal,axial}] [--silent] [--in_transparency_mask IN_TRANSPARENCY_MASK] [--output OUTPUT] [-f] [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}] [--sphere {repulsion100,symmetric362,repulsion724,symmetric642,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,ERROR}]] [--background BACKGROUND] [--bg_range MIN MAX] [--bg_opacity BG_OPACITY] [--bg_offset BG_OFFSET] [--bg_interpolation {nearest,linear}] [--bg_color BG_COLOR BG_COLOR BG_COLOR] [--peaks PEAKS] [--peaks_color PEAKS_COLOR PEAKS_COLOR PEAKS_COLOR] [--peaks_width PEAKS_WIDTH] [--peaks_opacity PEAKS_OPACITY] [--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. Note. The interactive visualization is not verified by tests. If you encounter any bug, please report it to our team or use --silent. 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 {image,trackball} 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 {repulsion100,symmetric362,repulsion724,symmetric642,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,ERROR}] 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 {nearest,linear} 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_opacity PEAKS_OPACITY Peaks opacity. 1 is opaque, 0 is transparent [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 (nifti). --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)] 2.2.2