List of MRtrix3 configuration file optionsΒΆ

  • AmbientIntensity

    default: 0.5

    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: 1.0,1.0,1.0

    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: 0.5

    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.

  • FontSize

    default: 10

    The size (in points) of the font to be used in OpenGL viewports (mrview and shview).

  • HelpCommand

    default: less

    The command to use to display each command’s help page (leave empty to send directly to the terminal).

  • IconSize

    default: 30

    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: 1.0,1.0,3.0

    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.

  • MRViewInitWindowSize

    default: 512,512

    Initial window size of MRView in pixels.

  • 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).

  • MRViewOdfScale

    default: 1.0

    The factor by which the ODF overlay is scaled.

  • 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.

  • NIFTI.AlwaysUseVer2

    default: 0 (false)

    A boolean value to indicate whether NIfTI images should always be written in the new NIfTI-2 format. If false, images will be written in the older NIfTI-1 format by default, with the exception being files where the number of voxels along any axis exceeds the maximum permissible in that format (32767), in which case the output file will automatically switch to the NIfTI-2 format.

  • NIfTI.AutoLoadJSON

    default: 0 (false)

    A boolean value to indicate whether, when opening NIfTI images, any corresponding JSON file should be automatically loaded.

  • NIfTI.AutoSaveJSON

    default: 0 (false)

    A boolean value to indicate whether, when writing NIfTI images, a corresponding JSON file should be automatically created in order to save any header entries that cannot be stored in the NIfTI header.

  • 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.

  • ScriptTmpDir

    default: `.`

    The location in which to generate the temporary directories to be used by MRtrix Python scripts. By default they will be generated in the working directory.

  • ScriptTmpPrefix

    default: `<script>-tmp-`

    The prefix to use when generating a unique name for a Python script temporary directory. By default the name of the invoked script itself will be used, followed by -tmp- (six random characters are then appended to produce a unique name in cases where a script may be run multiple times in parallel).

  • SparseDataInitialSize

    default: 16777216

    Initial buffer size for data in MRtrix sparse image format file (in bytes).

  • SpecularExponent

    default: 5.0

    The default exponent for the specular light in OpenGL renders.

  • SpecularIntensity

    default: 0.5

    The default intensity for the specular light in OpenGL renders.

  • TckgenEarlyExit

    default: 0 (false)

    Specifies whether tckgen should be terminated prematurely in cases where it appears as though the target number of accepted streamlines is not going to be met.

  • 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_coherence_len

    default: 3.0

    Linear registration: estimated spatial coherence length in voxels.

  • reg_gd_convergence_data_smooth

    default: 0.8

    Linear registration: control point trajectory smoothing value used in convergence check parameter range: [0...1].

  • reg_gd_convergence_min_iter

    default: 10

    Linear registration: minimum number of iterations until convergence check is activated.

  • reg_gd_convergence_slope_smooth

    default: 0.1

    Linear registration: control point trajectory slope smoothing value used in convergence check parameter range: [0...1].

  • reg_gd_convergence_thresh

    default: 5e-3

    Linear registration: threshold for convergence check using the smoothed control point trajectories measured in fraction of a 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 gradient descent step measured in fraction of a voxel at which to stop registration.