List of MRtrix3 configuration file optionsΒΆ
- AmbientIntensity
default: 0.6
The default intensity for the ambient light in OpenGL renders.
- AnalyseLeftToRight
default: 0 (false)
A boolean value to indicate whether images in Analyse format should be assumed to be in LAS orientation (default) or RAS (when this is option is turned on).
- BValueScaling
default: 1 (true)
Specifies whether the b-values should be scaled by the squared norm of the gradient vectors when loading a DW gradient scheme. This is commonly required to correctly interpret images acquired on scanners that nominally only allow a single b-value, as the common workaround is to scale the gradient vectors to modulate the actual b-value.
- BZeroThreshold
default: 10.0
Specifies the b-value threshold for determining those image volumes that correspond to b=0.
- BackgroundColor
default: 1,1,1 (white)
The default colour to use for the background in OpenGL panels, notably the SH viewer.
- ConnectomeEdgeAssociatedAlphaMultiplier
default: 1.0
The multiplicative factor to apply to the transparency of edges connected to one selected node.
- ConnectomeEdgeAssociatedColour
default: 0.0,0.0,0.0
The colour mixed in to edges connected to one currently selected node.
- ConnectomeEdgeAssociatedColourFade
default: 0.5
The fraction of the colour of an edge connected to one selected node determined by the fixed colour.
- ConnectomeEdgeAssociatedSizeMultiplier
default: 1.0
The multiplicative factor to apply to the size of edges connected to one selected node.
- ConnectomeEdgeOtherAlphaMultiplier
default: 1.0
The multiplicative factor to apply to the transparency of edges not connected to any selected node.
- ConnectomeEdgeOtherColour
default: 0.0,0.0,0.0
The colour mixed in to edges not connected to any currently selected node.
- ConnectomeEdgeOtherColourFade
default: 0.75
The fraction of the colour of an edge not connected to any selected node determined by the fixed colour.
- ConnectomeEdgeOtherSizeMultiplier
default: 1.0
The multiplicative factor to apply to the size of edges not connected to any selected node.
- ConnectomeEdgeOtherVisibilityOverride
default: true
Whether or not to force invisibility of edges not connected to any selected node.
- ConnectomeEdgeSelectedAlphaMultiplier
default: 1.0
The multiplicative factor to apply to the transparency of edges connected to two selected nodes.
- ConnectomeEdgeSelectedColour
default: 0.9,0.9,1.0
The colour used to highlight the edges connected to two currently selected nodes.
- ConnectomeEdgeSelectedColourFade
default: 0.5
The fraction of the colour of an edge connected to two selected nodes determined by the fixed selection highlight colour.
- ConnectomeEdgeSelectedSizeMultiplier
default: 1.0
The multiplicative factor to apply to the size of edges connected to two selected nodes.
- ConnectomeEdgeSelectedVisibilityOverride
default: false
Whether or not to force visibility of edges connected to two selected nodes.
- ConnectomeNodeAssociatedAlphaMultiplier
default: 1.0
The multiplicative factor to apply to the transparency of nodes associated with a selected node.
- ConnectomeNodeAssociatedColour
default: 0.0,0.0,0.0
The colour mixed in to those nodes associated with any selected node.
- ConnectomeNodeAssociatedColourFade
default: 0.5
The fraction of the colour of an associated node determined by the fixed associated highlight colour.
- ConnectomeNodeAssociatedSizeMultiplier
default: 1.0
The multiplicative factor to apply to the size of nodes associated with a selected node.
- ConnectomeNodeOtherAlphaMultiplier
default: 1.0
The multiplicative factor to apply to the transparency of nodes not currently selected nor associated with a selected node.
- ConnectomeNodeOtherColour
default: 0.0,0.0,0.0
The colour mixed in to those nodes currently not selected nor associated with any selected node.
- ConnectomeNodeOtherColourFade
default: 0.75
The fraction of the colour of an unselected, non-associated node determined by the fixed not-selected highlight colour.
- ConnectomeNodeOtherSizeMultiplier
default: 1.0
The multiplicative factor to apply to the size of nodes not currently selected nor associated with a selected node.
- ConnectomeNodeOtherVisibilityOverride
default: false
Whether or not nodes are forced to be invisible when not selected or associated with any selected node.
- ConnectomeNodeSelectedAlphaMultiplier
default: 1.0
The multiplicative factor to apply to the transparency of selected nodes.
- ConnectomeNodeSelectedColour
default: 1.0,1.0,1.0
The colour used to highlight those nodes currently selected.
- ConnectomeNodeSelectedColourFade
default: 0.75
The fraction of the colour of a selected node determined by the fixed selection highlight colour.
- ConnectomeNodeSelectedSizeMultiplier
default: 1.0
The multiplicative factor to apply to the size of selected nodes.
- ConnectomeNodeSelectedVisibilityOverride
default: true
Whether or not nodes are forced to be visible when selected.
- DiffuseIntensity
default: 0.3
The default intensity for the diffuse light in OpenGL renders.
- FailOnWarn
default: 0 (false)
A boolean value specifying whether MRtrix applications should abort as soon as any (otherwise non-fatal) warning is issued.
- HelpCommand
default: less
The command to use to display each command’s help page (leave empty to send directly to the terminal).
- IconSize
default: 24
The size of the icons in the main MRView toolbar.
- ImageInterpolation
default: true
Define default interplation setting for image and image overlay.
- ImageInterpolation
default: true
Interpolation switched on in the main image
- InitialToolBarPosition
default: top
The starting position of the MRView toolbar. Valid values are: top, bottom, left, right.
- LightPosition
default: 1,1,3
The default position vector to use for the light in OpenGL renders.
- MRViewColourBarHeight
default: 100
The height of the colourbar in MRView, in pixels.
- MRViewColourBarInset
default: 20
How far away from the edge of the main window to place the colourbar in MRView, in pixels.
- MRViewColourBarPosition
default: bottomright
The position of the colourbar within the main window in MRView. Valid values are: bottomleft, bottomright, topleft, topright.
- MRViewColourBarTextOffset
default: 10
How far away from the colourbar to place the associated text, in pixels.
- MRViewColourBarWidth
default: 20
The width of the colourbar in MRView, in pixels.
- MRViewColourHorizontalPadding
default: 100
The width in pixels between horizontally adjacent colour bars.
- MRViewDockFloating
default: 0 (false)
Whether MRView tools should start docked in the main window, or floating (detached from the main window).
- MRViewFocusModifierKey
default: meta (cmd on MacOSX)
Modifier key to select focus mode in MRView. Valid choices include shift, alt, ctrl, meta (on MacOSX: shift, alt, ctrl, cmd).
- MRViewImageBackgroundColour
default: 0,0,0 (black)
The default image background colour in the main MRView window.
- MRViewMaxNumColourmapRows
default: 3
The maximal number of rows used to layout a collection of rendered colourbars Note, that all tool-specific colourbars will form a single collection.
- MRViewMoveModifierKey
default: shift
Modifier key to select move mode in MRView. Valid choices include shift, alt, ctrl, meta (on MacOSX: shift, alt, ctrl, cmd).
- MRViewRotateModifierKey
default: ctrl
Modifier key to select rotate mode in MRView. Valid choices include shift, alt, ctrl, meta (on MacOSX: shift, alt, ctrl, cmd).
- MRViewShowColourbar
default: true
Colourbar shown in main image overlay
- MRViewShowComments
default: true
Comments shown in main image overlay
- MRViewShowFocus
default: true
Focus cross hair shown in main image
- MRViewShowOrientationLabel
default: true
Anatomical orientation information shown in main image overlay
- MRViewShowVoxelInformation
default: true
Voxel information shown in main image overlay
- MRViewToolFontSize
default: 2 points less than the standard system font
The point size for the font to use in MRView tools.
- MRViewToolsColourBarPosition
default: topright
The position of all visible tool colourbars within the main window in MRView. Valid values are: bottomleft, bottomright, topleft, topright.
- MSAA
default: 0 (false)
How many samples to use for multi-sample anti-aliasing (to improve display quality).
- NIFTI.AllowBitwise
default: 0 (false)
A boolean value to indicate whether bitwise storage of binary data is permitted (most 3rd party software packages don’t support bitwise data). If false (the default), data will be stored using more widely supported unsigned 8-bit integers.
- NeedOpenGLCoreProfile
default: 1 (true)
Whether the creation of an OpenGL 3.3 context requires it to be a core profile (needed on newer versions of the ATI drivers on Linux, for instance).
- NumberOfThreads
default: number of threads provided by hardware
Set the default number of CPU threads to use for multi-threading.
- NumberOfUndos
default: 16
The number of undo operations permitted in the MRView ROI editor tool.
- ObjectColor
default: 1,1,0 (yellow)
The default colour to use for objects (i.e. SH glyphs) when not colouring by direction.
- SparseDataInitialSize
default: 16777216
Initial buffer size for data in MRtrix sparse image format file (in bytes).
- SpecularExponent
default: 1
The default exponent for the specular light in OpenGL renders.
- SpecularIntensity
default: 0.4
The default intensity for the specular light in OpenGL renders.
- TerminalColor
default: 1 (true)
A boolean value to indicate whether colours should be used in the terminal.
- TmpFileDir
default: `/tmp` (on Unix), `.` (on Windows)
The prefix for temporary files (as used in pipelines). By default, these files get written to the current folder, which may cause performance issues when operating over distributed file systems. In this case, it may be better to specify /tmp/ here.
- TmpFilePrefix
default: `mrtrix-tmp-`
The prefix to use for the basename of temporary files. This will be used to generate a unique filename for the temporary file, by adding random characters to this prefix, followed by a suitable suffix (depending on file type). Note that this prefix can also be manipulated using the MRTRIX_TMPFILE_PREFIX environment variable, without editing the config file.
- ToolbarStyle
default: 2
The style of the main toolbar buttons in MRView. See Qt’s documentation for Qt::ToolButtonStyle.
- TrackWriterBufferSize
default: 16777216
The size of the write-back buffer (in bytes) to use when writing track files. MRtrix will store the output tracks in a relatively large buffer to limit the number of write() calls, avoid associated issues such as file fragmentation.
- VSync
default: 0 (false)
Whether the screen update should synchronise with the monitor’s vertical refresh (to avoid tearing artefacts).
- reg_analyse_descent
default: 0 (false)
Linear registration: write comma separated gradient descent parameters and gradients to stdout and verbose gradient descent output to stderr
- reg_bbgd
default: 1 (true)
Linear registration: use Barzilai Borwein gradient descent
- reg_coherence_len
default: 3.0
Linear registration: estimated spatial coherence length in voxel
- reg_gdweight_matrix
default: 0.0003
Linear registration: weight for optimisation of linear (3x3) matrix parameters
- reg_gdweight_translation
default: 1
Linear registration: weight for optimisation of translation parameters
- reg_stop_len
default: 0.0001
Linear registration: smallest step in fraction of voxel at which to stop registration