# List of MRtrix3 configuration file options¶

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).
BValueEpsilon

default: 80.0

Specifies the difference between b-values necessary for image volumes to be classified as belonging to different shells.
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.
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.
MRViewColourBarHorizontalPadding

default: 100

The width in pixels between horizontally adjacent colour bars.
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.
MRViewDefaultTractGeomType

default: Pseudotubes

The default geometry type used to render tractograms. Options are Pseudotubes, Lines or Points
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.
MRViewMaxNumColourBarRows

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.
MRViewOrthoAsRow

default: false

Display the 3 orthogonal views of the Ortho mode in a row, rather than as a 2x2 montage
MRViewRoiAlpha

default: 0.5

The default alpha of a ROI overlay.
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.
MRViewSyncFocus

default: false

Whether to sync the focus in mrview between other mrview processes.
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.
MRViewWrapVolumes

default: false

Wrap volumes around when cycling through
MSAA

default: 0 (false)

How many samples to use for multi-sample anti-aliasing (to improve display quality).
NIfTIAllowBitwise

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.
NIfTIAlwaysUseVer2

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.
NIfTIAutoLoadJSON

default: 0 (false)

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

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.
NIfTIUseSform

default: 1 (true)

A boolean value to control whether, in cases where both the sform and qform transformations are defined in an input NIfTI image, but those transformations differ, the sform transformation should be used in preference to the qform matrix. The default is to use the sform matrix; set to 0 / false to override and instead use the qform.
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

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.
RealignTransform

default: 1 (true)

A boolean value to indicate whether all images should be realigned to an approximately axial orientation at load.
RegAnalyseDescent

default: 0 (false)

Linear registration: write comma separated gradient descent parameters and gradients to stdout and verbose gradient descent output to stderr.
RegCoherenceLen

default: 3.0

Linear registration: estimated spatial coherence length in voxels.
RegGdConvergenceDataSmooth

default: 0.8

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

default: 10

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

default: 0.1

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

default: 5e-3

Linear registration: threshold for convergence check using the smoothed control point trajectories measured in fraction of a voxel.
RegGdWeightMatrix

default: 0.0003

Linear registration: weight for optimisation of linear (3x3) matrix parameters.
RegGdWeightTranslation

default: 1

Linear registration: weight for optimisation of translation parameters.
RegStopLen

default: 0.0001

Linear registration: smallest gradient descent step measured in fraction of a voxel at which to stop registration.
ScriptScratchDir

default: .

The location in which to generate the scratch directories to be used by MRtrix Python scripts. By default they will be generated in the working directory. Note that this setting does not influence the location in which piped images and other temporary files are created by MRtrix3; that is determined based on config file option TmpFileDir.
ScriptScratchPrefix

default: <script>-tmp-

The prefix to use when generating a unique name for a Python script scratch 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 on Windows machines, which may cause performance issues, particularly when operating over distributed file systems. On Unix machines, the default is /tmp/, which is typically a RAM file system and should therefore be fast; but may cause issues on machines with little RAM capacity or where write-access to this location is not permitted.

Note that this location can also be manipulated using the MRTRIX_TMPFILE_DIR environment variable, without editing the config file. Note also that this setting does not influence the location in which Python scripts construct their scratch directories; that is determined based on config file option ScriptScratchDir.

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).