usage: __main__.py [-h] [--volume_cmap_name VOLUME_CMAP_NAME]
[--volume_opacity VOLUME_OPACITY]
[--transparency TRANSPARENCY] [--slices SID [SID ...]]
[--axis {sagittal,coronal,axial}] [--size WIDTH HEIGHT]
[--display_slice_number] [--display_lr]
[--labelmap LABELMAP]
[--labelmap_cmap_name LABELMAP_CMAP_NAME]
[--labelmap_opacity LABELMAP_OPACITY]
[--overlays OVERLAYS [OVERLAYS ...]]
[--overlays_as_contours]
[--overlays_colors R G B [R G B ...]]
[--overlays_opacity OVERLAYS_OPACITY]
[--peaks PEAKS [PEAKS ...]] [--peaks_width PEAKS_WIDTH]
[--peaks_opacity PEAKS_OPACITY] [-v [{DEBUG,INFO,WARNING}]]
volume out_fname
Take screenshot(s) of one or more slices in a given image volume along the
requested axis. If slice indices are not provided, all slices in the volume
are used. The name of the output images are suffixed with _slice_{id}, with
id being the slice number in the volume. If a labelmap image is provided (e.g.
a tissue segmentation map), it is overlaid on the volume slices. Same goes if
a mask is provided, with the difference that it can be rendered as a
transparency overlay as well as a contour.
A labelmap image can be provided as the image volume, without requiring it as
the optional argument if only the former needs to be plot.
Example:
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_axial_annotated.png
--display_slice_number --display_lr
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_axial_masked.png
--transparency brainmask.nii.gz
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_axial.png
--slices 30 40 50 60 70 80 90 100
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_sagittal.png --axis sagittal
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_axial_plasma_cmap.png
--slices 30 40 50 60 70 80 90 100 --volume_cmap_name plasma
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_mask_overlay.png
--slices 30 40 50 60 70 80 90 100 --overlays brain_mask.nii.gz
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_mask_contour.png
--slices 30 40 50 60 70 80 90 100
--overlays brain_mask.nii.gz --overlays_as_contours
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_axial_tissue_map.png
--slices 30 40 50 60 70 80 90 100 --labelmap tissue_map.nii.gz
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_axial_tissue_viridis_cmap.png
--slices 30 40 50 60 70 80 90 100
--labelmap tissue_map.nii.gz --labelmap_cmap_name viridis
>>> scil_viz_volume_screenshot.py t1.nii.gz t1_axial_peaks.png
--slices 30 40 50 60 70 80 90 100 --peaks peaks.nii.gz --volume_opacity 0.5
positional arguments:
volume Input 3D Nifti file (.nii/.nii.gz).
out_fname Name of the output image(s). If multiple slices are provided (or none), their index will be append to the name (e.g. volume.jpg, volume.png becomes volume_slice_0.jpg, volume_slice_0.png).
options:
-h, --help show this help message and exit
--transparency TRANSPARENCY
Transparency Nifti image (.nii/.nii.gz). Can either be a binary mask or a scalar image in the range [0, 1].
--size WIDTH HEIGHT Size of the output image. [(768, 768)]
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
Slicing:
--slices SID [SID ...]
Slice indices to screenshot. If None are supplied, all slices inside the transparency mask are selected.
--axis {sagittal,coronal,axial}
Name of the axis to visualize. [axial]
Input overlays:
--labelmap LABELMAP Input labelmap file (.nii/.nii.gz).
--overlays OVERLAYS [OVERLAYS ...]
3D Nifti image(s) to overlay (.nii/.nii.gz).
--peaks PEAKS [PEAKS ...]
Peaks Nifti image (.nii/.nii.gz).
Volume rendering:
--volume_cmap_name VOLUME_CMAP_NAME
Colormap name for the 3D Nifti image data. [None]
--volume_opacity VOLUME_OPACITY
Opacity value for the 3D Nifti image data. [1.0]
--labelmap_cmap_name LABELMAP_CMAP_NAME
Colormap name for the labelmap image data. [viridis]
--labelmap_opacity LABELMAP_OPACITY
Opacity value for the labelmap image data. [0.5]
Peaks rendering:
--peaks_width PEAKS_WIDTH
Width of the peaks lines. [3.0]
--peaks_opacity PEAKS_OPACITY
Opacity value for the peaks overlay. [1.0]
Overlay rendering:
--overlays_as_contours
Display overlays contours and reduce the opacity of their inner region (see the `--overlays_opacity` argument).
--overlays_colors R G B [R G B ...]
Colors for the overlays or contours. You may provide a single color, for all overlays/contours, or one color for each. Each color is given as three values: R G B
--overlays_opacity OVERLAYS_OPACITY
Opacity value for the masks overlays. When combined with `--overlays_as_contours`, this will be the opacity of the region inside the computed contours. [0.5]
Annotations:
--display_slice_number
If true, displays the slice number in the upper left corner.
--display_lr If true, add left and right annotations to the images.