mrview

Synopsis

The MRtrix image viewer

Usage

mrview [ options ] [ image ... ]
  • image: An image to be loaded.

Description

Any images listed as arguments will be loaded and available through the image menu, with the first listed displayed initially. Any subsequent command-line options will be processed as if the corresponding action had been performed through the GUI.

Note that because images loaded as arguments (i.e. simply listed on the command-line) are opened before the GUI is shown, subsequent actions to be performed via the various command-line options must appear after the last argument. This is to avoid confusion about which option will apply to which image. If you need fine control over this, please use the -load or -select_image options. For example:

$ mrview -load image1.mif -interpolation 0 -load image2.mif -interpolation 0

or

$ mrview image1.mif image2.mif -interpolation 0 -select_image 2 -interpolation 0

Options

View options

  • -mode index (multiple uses permitted) Switch to view mode specified by the integer index, as per the view menu.
  • -load image (multiple uses permitted) Load image specified and make it current.
  • -reset (multiple uses permitted) Reset the view according to current image. This resets the FOV, projection and focus.
  • -fov value (multiple uses permitted) Set the field of view, in mm.
  • -focus x,y,z or boolean (multiple uses permitted) Either set the position of the crosshairs in scanner coordinates, with the new position supplied as a comma-separated list of floating-point values or show or hide the focus cross hair using a boolean value as argument.
  • -target x,y,z Set the target location for the viewing window (the scanner coordinate that will appear at the centre of the viewing window
  • -voxel x,y,z (multiple uses permitted) Set the position of the crosshairs in voxel coordinates, relative the image currently displayed. The new position should be supplied as a comma-separated list of floating-point values.
  • -volume idx (multiple uses permitted) Set the volume index for the image displayed, as a comma-separated list of integers.
  • -plane index (multiple uses permitted) Set the viewing plane, according to the mappping 0: sagittal; 1: coronal; 2: axial.
  • -lock yesno (multiple uses permitted) Set whether view is locked to image axes (0: no, 1: yes).
  • -select_image index (multiple uses permitted) Switch to image number specified, with reference to the list of currently loaded images.
  • -autoscale (multiple uses permitted) Reset the image scaling to automatically determined range.
  • -interpolation boolean (multiple uses permitted) Enable or disable image interpolation in main image.
  • -colourmap index (multiple uses permitted) Switch the image colourmap to that specified, as per the colourmap menu.
  • -noannotations (multiple uses permitted) Hide all image annotation overlays
  • -comments boolean (multiple uses permitted) Show or hide image comments overlay.
  • -voxelinfo boolean (multiple uses permitted) Show or hide voxel information overlay.
  • -orientationlabel boolean (multiple uses permitted) Show or hide orientation label overlay.
  • -colourbar boolean (multiple uses permitted) Show or hide colourbar overlay.
  • -imagevisible boolean (multiple uses permitted) Show or hide the main image.
  • -intensity_range min,max (multiple uses permitted) Set the image intensity range to that specified.

Window management options

  • -size width,height (multiple uses permitted) Set the size of the view area, in pixel units.
  • -position x,y (multiple uses permitted) Set the position of the main window, in pixel units.
  • -fullscreen Start fullscreen.
  • -exit Quit MRView.

Debugging options

  • -fps Display frames per second, averaged over the last 10 frames. The maximum over the last 3 seconds is also displayed.

Other options

  • -norealign do not realign transform to near-default RAS coordinate system (the default behaviour on image load). This is useful to inspect the image and/or header contents as they are actually stored in the header, rather than as MRtrix interprets them.

Overlay tool options

  • -overlay.load image (multiple uses permitted) Loads the specified image on the overlay tool.
  • -overlay.opacity value (multiple uses permitted) Sets the overlay opacity to floating value [0-1].
  • -overlay.colourmap index (multiple uses permitted) Sets the colourmap of the overlay as indexed in the colourmap dropdown menu.
  • -overlay.colour R,G,B (multiple uses permitted) Specify a manual colour for the overlay, as three comma-separated values
  • -overlay.intensity Min,Max (multiple uses permitted) Set the intensity windowing of the overlay
  • -overlay.threshold_min value (multiple uses permitted) Set the lower threshold value of the overlay
  • -overlay.threshold_max value (multiple uses permitted) Set the upper threshold value of the overlay
  • -overlay.no_threshold_min (multiple uses permitted) Disable the lower threshold for the overlay
  • -overlay.no_threshold_max (multiple uses permitted) Disable the upper threshold for the overlay
  • -overlay.interpolation value (multiple uses permitted) Enable or disable overlay image interpolation.

ROI editor tool options

  • -roi.load image (multiple uses permitted) Loads the specified image on the ROI editor tool.
  • -roi.opacity value (multiple uses permitted) Sets the overlay opacity to floating value [0-1].
  • -roi.colour R,G,B (multiple uses permitted) Sets the colour of the ROI overlay

Tractography tool options

  • -tractography.load tracks (multiple uses permitted) Load the specified tracks file into the tractography tool.
  • -tractography.thickness value (multiple uses permitted) Line thickness of tractography display, [-1.0, 1.0], default is 0.0.
  • -tractography.geometry value (multiple uses permitted) The geometry type to use when rendering tractograms (options are: pseudotubes, lines, points)
  • -tractography.opacity value (multiple uses permitted) Opacity of tractography display, [0.0, 1.0], default is 1.0.
  • -tractography.slab value (multiple uses permitted) Slab thickness of tractography display, in mm. -1 to turn off crop to slab.
  • -tractography.lighting value (multiple uses permitted) Toggle the use of lighting of tractogram geometry
  • -tractography.tsf_load tsf (multiple uses permitted) Load the specified tractography scalar file.
  • -tractography.tsf_range RangeMin,RangeMax (multiple uses permitted) Set range for the tractography scalar file. Requires -tractography.tsf_load already provided.
  • -tractography.tsf_thresh ThresholdMin,ThesholdMax (multiple uses permitted) Set thresholds for the tractography scalar file. Requires -tractography.tsf_load already provided.

ODF tool options

  • -odf.load_sh image (multiple uses permitted) Loads the specified SH-based ODF image on the ODF tool.
  • -odf.load_tensor image (multiple uses permitted) Loads the specified tensor image on the ODF tool.
  • -odf.load_dixel image (multiple uses permitted) Loads the specified dixel-based image on the ODF tool.

Fixel plot tool options

  • -fixel.load image (multiple uses permitted) Load a fixel file (any file inside a fixel directory, or an old .msf / .msh legacy format file) into the fixel tool.

Connectome tool options

  • -connectome.init image Initialise the connectome tool using a parcellation image.
  • -connectome.load path (multiple uses permitted) Load a matrix file into the connectome tool.

Screen Capture tool options

  • -capture.folder path (multiple uses permitted) Set the output folder for the screen capture tool.
  • -capture.prefix string (multiple uses permitted) Set the output file prefix for the screen capture tool.
  • -capture.grab (multiple uses permitted) Start the screen capture process.

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
  • -debug display debugging messages.
  • -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).
  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).
  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.
  • -help display this information page and exit.
  • -version display version information and exit.

References

Tournier, J.-D.; Calamante, F. & Connelly, A. MRtrix: Diffusion tractography in crossing fiber regions. Int. J. Imaging Syst. Technol., 2012, 22, 53-66


Author: J-Donald Tournier (jdtournier@gmail.com), Dave Raffelt (david.raffelt@florey.edu.au), Robert E. Smith (robert.smith@florey.edu.au), Rami Tabbara (rami.tabbara@florey.edu.au), Max Pietsch (maximilian.pietsch@kcl.ac.uk), Thijs Dhollander (thijs.dhollander@gmail.com)

Copyright: Copyright (c) 2008-2019 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.