Command line interface
FSLeyes has a comprehensive command line interface. Nearly everything that you can control through the overlay display panel, and the view settings panel for orthographic/lightbox/3D views, can be set via the command line.
Overview
The FSLeyes command line interface follows this pattern:
fsleyes [options] file [displayOpts] file [displayOpts] ...
where:
optionsrefers to options which relate to FSLeyes layout, behaviour, orthographic/lightbox configuration, etc.displayOptsrefers to a group of options which are applied to thefilethat preceeds the group.
Help
To get a brief overview of the FSLeyes command line interface, which just displays basic options:
fsleyes --help
fsleyes -h
To get help on the full FSLeyes command line interface (warning: it is quite long!):
fsleyes --fullhelp
fsleyes -fh
To print the version of FSLeyes you are using:
fsleyes --version
fsleyes -V
See below for the full FSLeyes help text.
Useful command line options
What follows is a short list highlighting some of the features in FSLeyes that you can access through the command line interface. For full details, refer to the command line help.
Initial display range
Auto-display
fsleyes --autoDisplay files ...
fsleyes -ad files ...
The --autoDisplay option tells FSLeyes to automatically configure certain
display properties when you load an overlay. For example, if you start FSLeyes
with --autoDisplay, and then load some Z-statistic images from a
FEAT analysis, FSLeyes will set a colour map and threshold
value on the images.
As another example, loading a MELODIC analysis with
--autoDisplay enabled will cause FSLeyes to load a background image, and
to configure positive and negative colour maps on the melodic_IC image.
Initial display range
- ::
fsleyes –initialDisplayRange 0 1000 files … fsleyes -idr 0 1000 files … fsleyes -idr 25 75% files … fsleyes –robustRange files … fsleyes -rr files …
The --initialDisplayRange option tells FSLeyes to set the display range
for all loaded images to the specified minimum/maximum values. If the maximum
value ends with a percent sign (%), the values are interpreted as
percentiles.
The --robustRange option tells FSLeyes to set the display range for all
loaded images to their “robust range”, as calculated by the fslstats -r
flag. If both the --initialDisplayRange and --robustRange options are
specified, only --initialDisplayRange will be applied.
Both the --initialDisplayRange and --robustRange options are only
applied to normal volume overlays.
Add standard
fsleyes --standard files ...
fsleyes --standard1mm files ...
fsleyes -std files ...
fsleyes -std1mm files ...
The --standard and --standard1mm options respectively tell FSLeyes to
load 2mm and 1mm versions of the MNI152 template. These options only work if
your command line environment has been correctly configured to use FSL
(e.g. the $FSLDIR environment variable is set).
Layouts
fsleyes --scene feat files ...
fsleyes --scene melodic files ...
fsleyes --scene default files ...
fsleyes --scene ortho files ...
fsleyes --scene lightbox files ...
fsleyes -s feat files ...
fsleyes -s melodic files ...
fsleyes -s default files ...
fsleyes -s ortho files ...
fsleyes -s lightbox files ...
The --scene option allows you to tell FSLeyes to start up with a specific
layout. If you have saved your
own custom layout, you can also load it, by name, using the --scene
option.
Font size
You can set the font used throughout the FSLeyes interface via the
--fontSize argument:
fsleyes --fontSize 6 files ...
fsleyes -fs 14 files ...
Neurological orientation
fsleyes --neuroOrientation files ...
fsleyes -no files ...
By default, FSLeyes displays images in radiological orientation (i.e. with
subject right to the left of the display, and subject left to the right). You
can use the --neuroOrientation option to tell FSLeyes to use neurological
orientation instead.
Force-load images
fsleyes --bigmem files ...
fsleyes -b files ...
By default, FSLeyes keeps large compressed NIFTI files on disk, only decompressing and loading data on-demand (i.e. when it needs to be viewed). While this reduces the amount of RAM needed to view such images, it also slows down the performance of changing volumes (e.g. via movie mode) and of viewing time series.
If you are using a computer with a large amount of RAM, and you don’t mind
loading the entire image into memory, you can use the --bigmem argument to
tell FSLeyes to do just that.
Run script
fsleyes --runscript script.py files ...
fsleyes -r script.py files ...
FSLeyes has a programming interface which you can use to programmatically set
up complex scenes. The --runscript option allows you to execute a Python
script when FSLeyes starts, which can load overlays and configure their
display properties, and set up the FSLeyes interface. These scripts have
access to the same environment that is available via the FSLeyes-Jupyter
notebook.
One FSLeyes instance
By default, when you call fsleyes on the command line, a new FSLeyes
instance will be opened. If you would prefer to have just one instance of
FSLeyes open, you can use the --cliserver option:
fsleyes --cliserver ...
fsleyes -cs ...
The first time you call fsleyes in this way, the FSLeyes application will
open as normal. Then, on subsequent calls, all of the arguments that you
specify on the command-line will be passed to that first instance. Note that
only overlay arguments will be applied on subsequent calls - all arguments
pertaining to the FSLeyes layout or displayed scene will be ignored.
If you would like FSLeyes to behave this way permanently, you can add it as a
default argument. Alternatively, you
could an alias to your shell startup file (e.g. ~/.bash_profile or
~/.zprofile):
alias fsleyes="fsleyes --cliserver"
Default command-line arguments
If you would like some command-line arguments to always be applied when you
start FSLeyes, you can store them in a file called default_arguments.txt,
located in the FSLeyes settings directory or the FSLeyes site
configuration directory. This file may
contain “global” command-line arguments (referred to as [options]
above), such as --autoDisplay,
--cliserver, etc. Empty lines, and lines beginning with # in this file
are ignored. An example default_arguments.txt file may look like this:
# Increase the default font size
--fontSize 18
# Start a single FSLeyes instance
--cliserver
# Default to displaying in neurological orientation
-no
Generating command line arguments
The orthographic, lightbox and 3D views have the ability to generate a command line which describes the currently displayed scene. This is available in the View sub-menu for each of these views, as the Show command line for scene option. These views also have a Apply command line arguments option, which allows you to paste in a previosuly generated command line.
Examples
Volume overlays
Set up display/clipping/colourmap/interpolation on an image, and centre display at a specific voxel:
fsleyes -sortho -std1mm -vl 33 20 31 \
zstat1.nii.gz -dr 2.5 3.5 -cr 2.5 3.5 -cm hot -in spline
Set up positive/negative colour map on a PE image:
fsleyes -std1mm pe1 -un -cm red-yellow \
-nc blue-lightblue -dr 10 60 -in spline
Vector overlays
Display dtifit output as an RGB vector:
fsleyes dti_FA dti_V1 -ot rgbvector
Display bedpostx two-fibre output as line vectors:
fsleyes mean_f1samples dyads1 -ot linevector dyads2_thr0.05 -ot linevector
Display dtifit output as a tensor (not possible in a SSH/X11 session).
You can specify the dtifit output directory:
fsleyes dtifit/dti_FA dtifit/
Or the 6-volume image containing the unique elements of the tensor matrix:
fsleyes dtifit/dti_FA dtifit/dti_tensor.nii.gz -ot tensor
Display spherical harmonic coefficients (not possible in a SSH/X11 session):
fsleyes asym_fods.nii.gz -ot sh
Melodic mode
Specify the path to your filtered_func_data.ica directory:
fsleyes -s melodic path/to/analysis.ica/filtered_func_data.ica
Or the path to your melodic_IC file:
fsleyes -s melodic path/to/analysis.ica/filtered_func_data.ica/melodic_IC
Use the -ad flag (--autoDisplay) to automatically set up colour maps:
fsleyes -ad -s melodic path/to/analysis.ica/filtered_func_data.ica/melodic_IC
Lightbox view
Set Z axis (-zx Z) and slice spacing (-ss 0.1). The slice spacing must
be specified as a proportion of the full length of the Z axis, between 0 and
1:
fsleyes -slightbox -zx Z -ss 0.1 -std1mm
Set slice range (-zr 0 0.5). This is also specified as proportions between
0 and 1, along the Z axis:
fsleyes -slightbox -zx Z -ss 0.1 -zr 0 0.5 -std1mm
fsleyes -slightbox -zx Z -ss 0.1 -zr 0.5 1 -std1mm
fsleyes -slightbox -zx Z -ss 0.1 -zr 0.25 0.75 -std1mm
If you add the –asVoxels / -av option, you can specify the slice spacing and Z range as voxel coordinates, e.g.:
fsleyes -slightbox -av -zx Z -ss 2 -zr 0 91 -std1mm
Off-screen rendering
FSLeyes is capable of generating screenshots from the command line. This is useful, for example, if you need to generate a large number of PNG images for quality control purposes. Simply build a FSLeyes command line which generates the scene that you wish to view, and then tell FSLeyes to render the scene to a file.
You can access the FSLeyes off-screen renderer by passing the word render
as the first argument to FSLeyes:
fsleyes render ...
The fsleyes render command will also work on systems which do not have a
display (e.g. cluster nodes), as long as the osmesa library is available. In order to use
osmesa, you need to set the PYOPENGL_PLATFORM="osmesa" environment
variable.
You can access command line help in the same manner as described above:
fsleyes render --help
fsleyes render -h
fsleyes render --fullhelp
fsleyes render -fh
Using the off-screen renderer is nearly identical to using the standard
FSLeyes command line interface, but you may also
specify an output file (this will default to out.png if not specified):
fsleyes render [options] --outfile outfile file [displayOpts] ...
fsleyes render [options] -of outfile file [displayOpts] ...
You may also specify the size of the generated image, in pixels:
fsleyes render [options] --outfile outfile --size 800 600 file [displayOpts] ...
fsleyes render [options] -of outfile -sz 800 600 file [displayOpts] ...
When using the off-screen renderer, the --scene option, normally used to
specify a layout, allows you to choose
between generating a screenshot with an orthographic, lightbox, or 3D view:
fsleyes render --scene ortho --outfile outfile file [displayOpts] ...
fsleyes render --scene lightbox --outfile outfile file [displayOpts] ...
fsleyes render --scene 3d --outfile outfile file [displayOpts] ...
FSLeyes command-line reference
Below you will find the full FSLeyes command-line reference - you can view
this locally by running fsleyes --fullhelp or fsleyes -fh.
FSLeyes version 1.18.0
Usage: fsleyes [options] file [displayOpts] file [displayOpts] ...
FSLeyes - the FSL image viewer.
Use the "--scene" option to load a saved layout (default, defaultlb, default3d,
melodic, feat, ortho, 3d, lightbox)
If no "--scene" is specified, a default layout is shown or the previous layout
is restored. If a script is provided via the "--runscript" argument, it is
assumed that the script sets up the scene.
Main options:
-r SCRIPTFILE, --runscript SCRIPTFILE
Run custom FSLeyes script
-cs, --cliserver Pass all command-line arguments to a single FSLeyes
instance
-h, --help Display basic FSLeyes options and exit
-fh, --fullhelp Display all FSLeyes options and exit
-v, --verbose Verbose output (can be used up to 3 times)
-V, --version Print the current version and exit
-S, --skipfslcheck Skip $FSLDIR check/warning
-U, --updatecheck Check for FSLeyes updates on startup
-n MODULE, --noisy MODULE
Make the specified module noisy
-gl MAJOR MINOR, --glversion MAJOR MINOR
Desired (major, minor) OpenGL compatibility version
-s SCENE, --scene SCENE
Scene to show
-vl X Y Z, --voxelLoc X Y Z
Location to show (voxel coordinates of first overlay)
-wl X Y Z, --worldLoc X Y Z
Location to show (world coordinates, takes precedence
over --voxelLoc)
-o INDEX, --selectedOverlay INDEX
Selected overlay (index, starting from 0)
-u, --ungroupOverlays
Do not group overlays via the chainlink button
-ad, --autoDisplay Automatically configure overlay display settings
(unless any display settings are specified)
-ds DISPLAYSPACE, --displaySpace DISPLAYSPACE
Space in which all overlays are displayed - can be
"world", "scaledVoxels", "fslview", or a NIFTI image.
-no, --neuroOrientation
Display images in neurological orientation (default:
radiological)
-how, --hideOrientationWarnings
Hides location panel warnings when displaying images
of different FOVs or orientations.
-std, --standard Add the MNI152 2mm standard image as an underlay (only
if $FSLDIR is set).
-stdb, --standard_brain
Add the MNI152 brain-extracted 2mm standard image as
an underlay (only if $FSLDIR is set).
-std1mm, --standard1mm
Add the MNI152 1mm standard image as an underlay (only
if $FSLDIR is set).
-std1mmb, --standard1mm_brain
Add the MNI152 brain-extracted 1mm standard image as
an underlay (only if $FSLDIR is set).
-idr LO HI, --initialDisplayRange LO HI
Initial display range to use for volume overlays,
expressed as (low, high) intensity values. The values
can be expresseed as percentiles by appending a "%" to
the high value.
-rr, --robustRange Set the initial display range for volume overlays to
the "robust range" as calculated by fslstats. Ignored
if --initialDisplayRange is also specified. For 4D
images, the robust range is calculated on the first
volume. If fslstats is not available, the image data
range is used.
-cy, --cmapCycle Automatically assign a different colour map to each
volume overlay (unless one is explicitly specified).
-b, --bigmem Load all images into memory, regardless of size.
-fs FONTSIZE, --fontSize FONTSIZE
Application font size
-nb, --notebook Start the Jupyter notebook server
-nbf NOTEBOOKFILE, --notebookFile NOTEBOOKFILE
Start the Jupyter notebook server and open the
specified notebook file.
-nbp NOTEBOOKPORT, --notebookPort NOTEBOOKPORT
Jupyter notebook server port
-nbb, --noBrowser Start the jupyter notebook server, but do not open the
Jupyter notebook home page in a web browser.
-a ANNOTATIONS, --annotations ANNOTATIONS
Load annotations from file (only applied to ortho
views)
-ni, --no3DInterp Do not automatically enable interpolation for volume
overlays when opening a 3D view
-ap, --showAllPlugins
Expose plugins from third party packages
-an, --autoName Automatically give each overlay a unique name based on
its file path
Scene options:
These settings are applied to every orthographic, lightbox, and 3D view.
-hc, --hideCursor Do not display the green cursor highlighting the
current location
-cw REAL, --cursorWidth REAL
Location cursor thickness
-bg R G B, --bgColour R G B
Canvas background colour (0-1)
-fg R G B, --fgColour R G B
Canvas foreground colour (0-1)
-cc R G B, --cursorColour R G B
Cursor location colour (0-1)
-cb, --showColourBar Show colour bar
-cbl {top,bottom,left,right}, --colourBarLocation {top,bottom,left,right}
Colour bar location
-cbs {top-left,bottom-right}, --colourBarLabelSide {top-left,bottom-right}
Colour bar label orientation
-cbi PERC, --colourBarSize PERC
Colour bar size (%)
-ls INT, --labelSize INT
Orientation/colour bar label font size (4-96, default:
12)
-p {1,2,3}, --performance {1,2,3}
Rendering performance (1=fastest, 2=faster, 3=best
looking)
-ms, --movieSync Toggle the canvas refresh strategy in movie mode.
Ortho display options:
These settings are applied to every ortho view.
-xz PERC, --xzoom PERC
X canvas zoom (100-5000, default: 100)
-yz PERC, --yzoom PERC
Y canvas zoom (100-5000, default: 100)
-zz PERC, --zzoom PERC
Z canvas zoom (100-5000, default: 100)
-cg, --cursorGap Show a gap at the cursor centre
-hl, --hideLabels Hide orientation labels
-sl {no,X,Y,Z}, --showLocation {no,X,Y,Z}
Show cursor location coordinates
-lo {horizontal,vertical,grid}, --layout {horizontal,vertical,grid}
Canvas layout
-xh, --hidex Hide the X canvas
-yh, --hidey Hide the Y canvas
-zh, --hidez Hide the Z canvas
-ixv, --invertXVertical
Invert the X canvas along the vertical axis
-ixh, --invertXHorizontal
Invert the X canvas along the horizontal axis
-iyv, --invertYVertical
Invert the Y canvas along the vertical axis
-iyh, --invertYHorizontal
Invert the Y canvas along the horizontal axis
-izv, --invertZVertical
Invert the Z canvas along the vertical axis
-izh, --invertZHorizontal
Invert the Z canvas along the horizontal axis
-xc Y Z, --xcentre Y Z
X canvas centre ([-1, 1])
-yc X Z, --ycentre X Z
Y canvas centre ([-1, 1])
-zc X Y, --zcentre X Y
Z canvas centre ([-1, 1])
LightBox display options:
These settings are applied to every lightbox view.
-zx {2,0,1,z,Z,x,X,y,Y}, --zaxis {2,0,1,z,Z,x,X,y,Y}
Z axis
-zr LO HI, --zrange LO HI
Slice range, specified as proportions between 0 and 1,
or as voxel coordinates if --asVoxels is provided.
-ss REAL, --sliceSpacing REAL
Slice spacing, specified as a proportion between 0 and
1, or as voxel coordinates if --asVoxels is provided.
-sa {centre,start}, --sampleSlices {centre,start}
Control how slices are sampled (either "centre" or
"start").
-sg, --showGridLines Show grid lines
-hs, --highlightSlice
Highlight current slice
-sp {none,voxel,world}, --labelSpace {none,voxel,world}
Show slice locations in this coordinate system.
-rs, --reverseSlices Display slices from high to low Z value, instead of
low to high.
-so PERC, --sliceOverlap PERC
Overlap adjacent slices by this much, specified as a
percentage.
-ro, --reverseOverlap
Draw lower slices on top of higher slices instead of
higher on top of lower.
-av, --asVoxels Causes the --zrange and --sliceSpacing settings to be
interpreted as voxel coordinates. Has no effect if
--zrange is not provided.
-ns N, --numSlices N Number of slices. Ignored if --sliceSpacing is
specified.
-ll, --sliceLocation Show location in world coordinates on each slice.
Ignored if --labelSpace is specified
3D display options:
These settings are applied to every 3D view.
-z PERC, --zoom PERC Zoom (1-5000, default: 100)
-he, --hideLegend Hide the orientation legend
-dl, --disableLight Disable light effect
-lp N N N, --lightPos N N N
Light position, as XYZ rotations in degrees (-180 -
180)
-ld REAL, --lightDistance REAL
Distance of light source from centre of display
bounding box (0.5 - 10)
-off N N, --offset N N
Offset from centre ([-1, 1])
-rot YAW PITCH ROLL, --cameraRotation YAW PITCH ROLL
Rotation (degrees), specified as yaw (rotation about
the vertical axis), pitch (rotation about the
horizontal axis) and roll (rotation about the depth
axis).
###############
Display options
###############
Each display option will be applied to the overlay which is
listed before that option. Passing any display option for an
overlay will override the '--autoDisplay' setting for that
overlay.
-n NAME, --name NAME Overlay name
-d, --disabled Disable (hide) overlay
-ot TYPE, --overlayType TYPE
Overlay type
-a PERC, --alpha PERC
Opacity (0-100, default: 100)
-b PERC, --brightness PERC
Brightness (0-100, default: 50)
-c PERC, --contrast PERC
Contrast (0-100, default: 50)
Available overlay types: complex, label, linevector, mask, mesh, mip, rgb,
rgbvector, sh, tensor, tractogram, volume
##############
Volume options
##############
These options are applied to 'volume' overlays.
-ll, --unlinkLowRanges
Unlink low display/clipping ranges
-lh, --linkHighRanges
Link high display/clipping ranges
-or LO HI, --overrideDataRange LO HI
Override data range. Setting this effectively causes
FSLeyes to ignore the actual image data range, and use
this range instead. This is useful for images with a
large data range that is driven by outliers.
-cm CMAP, --cmap CMAP
Colour map
-nc CMAP, --negativeCmap CMAP
Colour map for negative values
-un, --useNegativeCmap
Use negative colour map (automatically enabled if
--negativeCmap is specified)
-dr LO HI, --displayRange LO HI
Display range. Setting this will override
brightnes/contrast settings. For volume overlays only:
append a "%" to the high value to set range by
percentile.
-cr LO HI, --clippingRange LO HI
Clipping range. Setting this will override the low
display range (unless low ranges are unlinked). For
volume overlays only: append a "%" to the high value
to clip by percentile.
-mr LO HI, --modulateRange LO HI
Modulate range. Sets the range by which opacity should
be modulated by. For volume overlays only: append a
"%" to the high value to modulate by percentile.
-g REAL, --gamma REAL
Gamma correction [-1-+1, default: 0]
-ls, --logScale Logarithmic scaling
-ch {R,G,B,A}, --channel {R,G,B,A}
Channel to display, for RGB(A) images
-ic, --invertClipping
Invert clipping
-cmr INT, --cmapResolution INT
Colour map resolution
-in {none,linear,spline,true_spline}, --interpolation {none,linear,spline,true_spline}
Interpolation
-inc, --interpolateCmaps
Interpolate between colours in colour maps
-i, --invert Invert colour map
-ma, --modulateAlpha Modulate alpha by intensity
-ima, --invertModulateAlpha
no help
-ns INT, --numSteps INT
3D only. Maximum number of samples per pixel
-bf REAL, --blendFactor REAL
3D only Sample blending factor [0.001-1, default: 0.1]
-bi, --noBlendByIntensity
3D only. Disable modulation of sample colours by voxel
intensity when blending.
-s INT, --smoothing INT
3D only. Smoothing radius [0-10, default: 0]
-r INT, --resolution INT
3D only. Resolution/quality [1-100, default: 100]
-nis INT, --numInnerSteps INT
3D/GL14 only. Number of samples to run on GPU
-m {intersection,union,complement}, --clipMode {intersection,union,complement}
3D only. How to apply the clipping plane(s).
-v INT, --volume INT Volume (index, starting from 0).
-cl FILE, --clipImage FILE
Image containing clipping values (defaults to the
image itself)
-mi FILE, --modulateImage FILE
Image containing modulation values (defaults to the
image itself)
-cp POS AZI INC, --clipPlane POS AZI INC
3D only. Add a clipping plane. Requires three values:
position [0-100], azimuth [-180, 180], inclination
[-180, 180]. Can be used up to 10 times.
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
Available colour maps: blue, blue-lightblue, brain_colours_1hot,
brain_colours_1hot_iso, brain_colours_2winter, brain_colours_2winter_iso,
brain_colours_3warm, brain_colours_3warm_iso, brain_colours_4cool,
brain_colours_4cool_iso, brain_colours_5redyell, brain_colours_5redyell_iso,
brain_colours_6bluegrn, brain_colours_6bluegrn_iso, brain_colours_actc,
brain_colours_actc_iso, brain_colours_blackbdy, brain_colours_blackbdy_iso,
brain_colours_bluegray, brain_colours_bluegray_iso, brain_colours_bone,
brain_colours_bone_iso, brain_colours_cardiac, brain_colours_cardiac_iso,
brain_colours_cortex, brain_colours_cortex_iso, brain_colours_diverging_bgy,
brain_colours_diverging_bgy_iso, brain_colours_diverging_bwr,
brain_colours_diverging_bwr_iso, brain_colours_flow, brain_colours_flow_iso,
brain_colours_french, brain_colours_french_iso, brain_colours_ge_color,
brain_colours_ge_color_iso, brain_colours_gold, brain_colours_gold_iso,
brain_colours_gooch, brain_colours_gooch_iso, brain_colours_greengray,
brain_colours_greengray_iso, brain_colours_hotiron, brain_colours_hotiron_iso,
brain_colours_nih, brain_colours_nih_fire, brain_colours_nih_fire_iso,
brain_colours_nih_ice, brain_colours_nih_ice_iso, brain_colours_nih_iso,
brain_colours_nih_new, brain_colours_nih_new_iso, brain_colours_pink,
brain_colours_pink_iso, brain_colours_rainramp, brain_colours_rainramp_iso,
brain_colours_redgray, brain_colours_redgray_iso, brain_colours_spectrum,
brain_colours_spectrum_iso, brain_colours_surface, brain_colours_surface_iso,
brain_colours_x_hot, brain_colours_x_hot_iso, brain_colours_x_rain,
brain_colours_x_rain_iso, cool, copper, cortical, green, greyscale, hot, hsv,
pink, random, red, red-yellow, render1, render1t, render2, render2t, render3,
retino, subcortical, yellow. You can also specify any matplotlib colour map,
or a colour map file.
#####################
RGB(A) volume options
#####################
These options are applied to 'rgb' overlays.
-in {none,linear,spline,true_spline}, --interpolation {none,linear,spline,true_spline}
Interpolation
-rc R G B, --rColour R G B
R colour (0-1)
-gc R G B, --gColour R G B
G colour (0-1)
-bc R G B, --bColour R G B
B colour (0-1)
-rs, --suppressR Suppress R channel
-gs, --suppressG Suppress G channel
-bs, --suppressB Suppress B channel
-as, --suppressA Suppress A channel
-sm {white,black,transparent}, --suppressMode {white,black,transparent}
Replace suppressed channels with 'white' (default),
'black', or 'transparent'.
-v INT, --volume INT Volume (index, starting from 0).
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
######################
Complex volume options
######################
These options are applied to 'complex' overlays.
-co {real,imag,mag,phase}, --component {real,imag,mag,phase}
Component to display - real (default), imaginary,
magnitude, or phase.
-ll, --unlinkLowRanges
Unlink low display/clipping ranges
-lh, --linkHighRanges
Link high display/clipping ranges
-or LO HI, --overrideDataRange LO HI
Override data range. Setting this effectively causes
FSLeyes to ignore the actual image data range, and use
this range instead. This is useful for images with a
large data range that is driven by outliers.
-cm CMAP, --cmap CMAP
Colour map
-nc CMAP, --negativeCmap CMAP
Colour map for negative values
-un, --useNegativeCmap
Use negative colour map (automatically enabled if
--negativeCmap is specified)
-dr LO HI, --displayRange LO HI
Display range. Setting this will override
brightnes/contrast settings. For volume overlays only:
append a "%" to the high value to set range by
percentile.
-cr LO HI, --clippingRange LO HI
Clipping range. Setting this will override the low
display range (unless low ranges are unlinked). For
volume overlays only: append a "%" to the high value
to clip by percentile.
-mr LO HI, --modulateRange LO HI
Modulate range. Sets the range by which opacity should
be modulated by. For volume overlays only: append a
"%" to the high value to modulate by percentile.
-g REAL, --gamma REAL
Gamma correction [-1-+1, default: 0]
-ls, --logScale Logarithmic scaling
-ch {R,G,B,A}, --channel {R,G,B,A}
Channel to display, for RGB(A) images
-ic, --invertClipping
Invert clipping
-cmr INT, --cmapResolution INT
Colour map resolution
-in {none,linear,spline,true_spline}, --interpolation {none,linear,spline,true_spline}
Interpolation
-inc, --interpolateCmaps
Interpolate between colours in colour maps
-i, --invert Invert colour map
-ma, --modulateAlpha Modulate alpha by intensity
-ima, --invertModulateAlpha
no help
-ns INT, --numSteps INT
3D only. Maximum number of samples per pixel
-bf REAL, --blendFactor REAL
3D only Sample blending factor [0.001-1, default: 0.1]
-bi, --noBlendByIntensity
3D only. Disable modulation of sample colours by voxel
intensity when blending.
-s INT, --smoothing INT
3D only. Smoothing radius [0-10, default: 0]
-r INT, --resolution INT
3D only. Resolution/quality [1-100, default: 100]
-nis INT, --numInnerSteps INT
3D/GL14 only. Number of samples to run on GPU
-m {intersection,union,complement}, --clipMode {intersection,union,complement}
3D only. How to apply the clipping plane(s).
-v INT, --volume INT Volume (index, starting from 0).
-cl FILE, --clipImage FILE
Image containing clipping values (defaults to the
image itself)
-mi FILE, --modulateImage FILE
Image containing modulation values (defaults to the
image itself)
-cp POS AZI INC, --clipPlane POS AZI INC
3D only. Add a clipping plane. Requires three values:
position [0-100], azimuth [-180, 180], inclination
[-180, 180]. Can be used up to 10 times.
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
Available colour maps: blue, blue-lightblue, brain_colours_1hot,
brain_colours_1hot_iso, brain_colours_2winter, brain_colours_2winter_iso,
brain_colours_3warm, brain_colours_3warm_iso, brain_colours_4cool,
brain_colours_4cool_iso, brain_colours_5redyell, brain_colours_5redyell_iso,
brain_colours_6bluegrn, brain_colours_6bluegrn_iso, brain_colours_actc,
brain_colours_actc_iso, brain_colours_blackbdy, brain_colours_blackbdy_iso,
brain_colours_bluegray, brain_colours_bluegray_iso, brain_colours_bone,
brain_colours_bone_iso, brain_colours_cardiac, brain_colours_cardiac_iso,
brain_colours_cortex, brain_colours_cortex_iso, brain_colours_diverging_bgy,
brain_colours_diverging_bgy_iso, brain_colours_diverging_bwr,
brain_colours_diverging_bwr_iso, brain_colours_flow, brain_colours_flow_iso,
brain_colours_french, brain_colours_french_iso, brain_colours_ge_color,
brain_colours_ge_color_iso, brain_colours_gold, brain_colours_gold_iso,
brain_colours_gooch, brain_colours_gooch_iso, brain_colours_greengray,
brain_colours_greengray_iso, brain_colours_hotiron, brain_colours_hotiron_iso,
brain_colours_nih, brain_colours_nih_fire, brain_colours_nih_fire_iso,
brain_colours_nih_ice, brain_colours_nih_ice_iso, brain_colours_nih_iso,
brain_colours_nih_new, brain_colours_nih_new_iso, brain_colours_pink,
brain_colours_pink_iso, brain_colours_rainramp, brain_colours_rainramp_iso,
brain_colours_redgray, brain_colours_redgray_iso, brain_colours_spectrum,
brain_colours_spectrum_iso, brain_colours_surface, brain_colours_surface_iso,
brain_colours_x_hot, brain_colours_x_hot_iso, brain_colours_x_rain,
brain_colours_x_rain_iso, cool, copper, cortical, green, greyscale, hot, hsv,
pink, random, red, red-yellow, render1, render1t, render2, render2t, render3,
retino, subcortical, yellow. You can also specify any matplotlib colour map,
or a colour map file.
############
Mask options
############
These options are applied to 'mask' overlays.
-mc R G B, --maskColour R G B
Colour (0-1)
-i, --maskInvert Invert
-t LO HI, --threshold LO HI
Threshold
-o, --outline Show mask outline
-w INT, --outlineWidth INT
Mask outline width (1-10, default: 2)
-in {none,linear,spline,true_spline}, --interpolation {none,linear,spline,true_spline}
Interpolation
-v INT, --volume INT Volume (index, starting from 0).
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
#############
Label options
#############
These options are applied to 'label' overlays.
-l LUT, --lut LUT Label image LUT
-o, --outline Show label outlines
-w INT, --outlineWidth INT
Label outline width (proportion of one voxel; 0-1,
default: 0.25)
-v INT, --volume INT Volume (index, starting from 0).
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
Available lookup tables: freesurfercolorlut, harvard-oxford-cortical, harvard-
oxford-subcortical, melodic-classes, mgh-cma-freesurfer, paul_tol_accessible,
random, random_big. You can also specify a lookup table file.
############
Mesh options
############
These options are applied to 'mesh' overlays.
-vd FILE, --vertexData FILE
A file (e.g. Freesurfer .curv file, GIFTI functional,
shape, label, or time series file, or a plain text
file) containing one or more values for each vertex in
the mesh.
-vdi INT, --vertexDataIndex INT
If the vertex data (-vd/--vertexData) file contains
more than one value per vertex, specify the the index
of the data to display.
-vs FILE, --vertexSet FILE
A file containing an additional (compatible) mesh
definition.
-md FILE, --modulateData FILE
Vertex data file by which to modulate transparency by.
-mc R G B, --colour R G B
Mesh colour (0-1)
-o, --outline Show mesh outline
-w REAL, --outlineWidth REAL
Mesh outline width (0-20, default: 2)
-s {affine,pixdim,pixdim-flip,id,torig}, --coordSpace {affine,pixdim,pixdim-flip,id,torig}
Overlay vertex coordinate space (relative to reference
image)
-ul, --useLut Use a lookup table instead of colour map(s) when
colouring the mesh with vertex data.
-l LUT, --lut LUT Lookup table to use (see -ul/--useLut).
-ll, --unlinkLowRanges
Unlink low display/clipping ranges
-lh, --linkHighRanges
Link high display/clipping ranges
-un, --useNegativeCmap
Use negative colour map (automatically enabled if
--negativeCmap is specified)
-dr LO HI, --displayRange LO HI
Display range. Setting this will override
brightnes/contrast settings. For volume overlays only:
append a "%" to the high value to set range by
percentile.
-cr LO HI, --clippingRange LO HI
Clipping range. Setting this will override the low
display range (unless low ranges are unlinked). For
volume overlays only: append a "%" to the high value
to clip by percentile.
-mr LO HI, --modulateRange LO HI
Modulate range. Sets the range by which opacity should
be modulated by. For volume overlays only: append a
"%" to the high value to modulate by percentile.
-g REAL, --gamma REAL
Gamma correction [-1-+1, default: 0]
-dc, --discardClipped
Discard clipped regions, rather than colouring them
with the flat colour
-ic, --invertClipping
Invert clipping
-cm CMAP, --cmap CMAP
Colour map
-nc CMAP, --negativeCmap CMAP
Colour map for negative values
-cmr INT, --cmapResolution INT
Colour map resolution
-in {linear,nearest}, --interpolation {linear,nearest}
Interpolation method, when colouring a mesh with
vertex data.
-inc, --interpolateCmaps
Interpolate between colours in colour maps
-i, --invert Invert colour map
-ma, --modulateAlpha Modulate alpha by intensity
-ima, --invertModulateAlpha
no help
-wf, --wireframe 3D only. Draw as wireframe
-r FILE, --refImage FILE
Reference image for overlay
-f, --flatShading Deprecated - use the --interpolation option instead.
#####################
GIFTI surface options
#####################
These options are applied to 'mesh' overlays.
-vd FILE, --vertexData FILE
A file (e.g. Freesurfer .curv file, GIFTI functional,
shape, label, or time series file, or a plain text
file) containing one or more values for each vertex in
the mesh.
-vdi INT, --vertexDataIndex INT
If the vertex data (-vd/--vertexData) file contains
more than one value per vertex, specify the the index
of the data to display.
-vs FILE, --vertexSet FILE
A file containing an additional (compatible) mesh
definition.
-md FILE, --modulateData FILE
Vertex data file by which to modulate transparency by.
-mc R G B, --colour R G B
Mesh colour (0-1)
-o, --outline Show mesh outline
-w REAL, --outlineWidth REAL
Mesh outline width (0-20, default: 2)
-s {affine,pixdim,pixdim-flip,id,torig}, --coordSpace {affine,pixdim,pixdim-flip,id,torig}
Overlay vertex coordinate space (relative to reference
image)
-ul, --useLut Use a lookup table instead of colour map(s) when
colouring the mesh with vertex data.
-l LUT, --lut LUT Lookup table to use (see -ul/--useLut).
-ll, --unlinkLowRanges
Unlink low display/clipping ranges
-lh, --linkHighRanges
Link high display/clipping ranges
-un, --useNegativeCmap
Use negative colour map (automatically enabled if
--negativeCmap is specified)
-dr LO HI, --displayRange LO HI
Display range. Setting this will override
brightnes/contrast settings. For volume overlays only:
append a "%" to the high value to set range by
percentile.
-cr LO HI, --clippingRange LO HI
Clipping range. Setting this will override the low
display range (unless low ranges are unlinked). For
volume overlays only: append a "%" to the high value
to clip by percentile.
-mr LO HI, --modulateRange LO HI
Modulate range. Sets the range by which opacity should
be modulated by. For volume overlays only: append a
"%" to the high value to modulate by percentile.
-g REAL, --gamma REAL
Gamma correction [-1-+1, default: 0]
-dc, --discardClipped
Discard clipped regions, rather than colouring them
with the flat colour
-ic, --invertClipping
Invert clipping
-cm CMAP, --cmap CMAP
Colour map
-nc CMAP, --negativeCmap CMAP
Colour map for negative values
-cmr INT, --cmapResolution INT
Colour map resolution
-in {linear,nearest}, --interpolation {linear,nearest}
Interpolation method, when colouring a mesh with
vertex data.
-inc, --interpolateCmaps
Interpolate between colours in colour maps
-i, --invert Invert colour map
-ma, --modulateAlpha Modulate alpha by intensity
-ima, --invertModulateAlpha
no help
-wf, --wireframe 3D only. Draw as wireframe
-r FILE, --refImage FILE
Reference image for overlay
-f, --flatShading Deprecated - use the --interpolation option instead.
##########################
Freesurfer surface options
##########################
These options are applied to 'mesh' overlays.
-vd FILE, --vertexData FILE
A file (e.g. Freesurfer .curv file, GIFTI functional,
shape, label, or time series file, or a plain text
file) containing one or more values for each vertex in
the mesh.
-vdi INT, --vertexDataIndex INT
If the vertex data (-vd/--vertexData) file contains
more than one value per vertex, specify the the index
of the data to display.
-vs FILE, --vertexSet FILE
A file containing an additional (compatible) mesh
definition.
-md FILE, --modulateData FILE
Vertex data file by which to modulate transparency by.
-mc R G B, --colour R G B
Mesh colour (0-1)
-o, --outline Show mesh outline
-w REAL, --outlineWidth REAL
Mesh outline width (0-20, default: 2)
-s {affine,pixdim,pixdim-flip,id,torig}, --coordSpace {affine,pixdim,pixdim-flip,id,torig}
Overlay vertex coordinate space (relative to reference
image)
-ul, --useLut Use a lookup table instead of colour map(s) when
colouring the mesh with vertex data.
-l LUT, --lut LUT Lookup table to use (see -ul/--useLut).
-ll, --unlinkLowRanges
Unlink low display/clipping ranges
-lh, --linkHighRanges
Link high display/clipping ranges
-un, --useNegativeCmap
Use negative colour map (automatically enabled if
--negativeCmap is specified)
-dr LO HI, --displayRange LO HI
Display range. Setting this will override
brightnes/contrast settings. For volume overlays only:
append a "%" to the high value to set range by
percentile.
-cr LO HI, --clippingRange LO HI
Clipping range. Setting this will override the low
display range (unless low ranges are unlinked). For
volume overlays only: append a "%" to the high value
to clip by percentile.
-mr LO HI, --modulateRange LO HI
Modulate range. Sets the range by which opacity should
be modulated by. For volume overlays only: append a
"%" to the high value to modulate by percentile.
-g REAL, --gamma REAL
Gamma correction [-1-+1, default: 0]
-dc, --discardClipped
Discard clipped regions, rather than colouring them
with the flat colour
-ic, --invertClipping
Invert clipping
-cm CMAP, --cmap CMAP
Colour map
-nc CMAP, --negativeCmap CMAP
Colour map for negative values
-cmr INT, --cmapResolution INT
Colour map resolution
-in {linear,nearest}, --interpolation {linear,nearest}
Interpolation method, when colouring a mesh with
vertex data.
-inc, --interpolateCmaps
Interpolate between colours in colour maps
-i, --invert Invert colour map
-ma, --modulateAlpha Modulate alpha by intensity
-ima, --invertModulateAlpha
no help
-wf, --wireframe 3D only. Draw as wireframe
-r FILE, --refImage FILE
Reference image for overlay
-f, --flatShading Deprecated - use the --interpolation option instead.
###################
Line vector options
###################
These options are applied to 'linevector' overlays.
-of, --orientFlip Flip L/R orientation within each voxel. Default: true
for images with neurological storage order, false for
images with radiological storage order. Passing this
flag will invert the default behaviour.
-lw REAL, --lineWidth REAL
Line width (1-10, default: 1)
-ld, --directed Interpret vectors as directed
-nu, --notunit Do not scale lines to unit length
-ls PERC, --lengthScale PERC
Scale line length by this percentage (10-500, default:
100)
-cm CMAP, --cmap CMAP
Colour map (only used if a colour image is provided)
-or LO HI, --colourRange LO HI
Colour-by range (only used if a colour image is
provided)
-mr LO HI, --modulateRange LO HI
Modulation range (only used if a modulation image is
provided)
-mm {brightness,alpha,lineLength,lineWidth}, --modulateMode {brightness,alpha,lineLength,lineWidth}
Modulate vector 'brightness' (default), 'alpha',
'lineLength', or 'lineWidth'.
-cr LO HI, --clippingRange LO HI
Clipping range (only used if a clipping image is
provided)
-xc R G B, --xColour R G B
X colour (0-1)
-yc R G B, --yColour R G B
Y colour (0-1)
-zc R G B, --zColour R G B
Z colour (0-1)
-xs, --suppressX Suppress X magnitude
-ys, --suppressY Suppress Y magnitude
-zs, --suppressZ Suppress Z magnitude
-sm {white,black,transparent}, --suppressMode {white,black,transparent}
Replace suppressed colours with 'white' (default),
'black', or 'transparent'.
-nr, --normaliseColour
Normalise RGB values to uniform brigntness.
-co FILE, --colourImage FILE
Image to colour vectors with
-mo FILE, --modulateImage FILE
Image to modulate vector brightness/alpha with
-cl FILE, --clipImage FILE
Image to clip vectors with
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
##################
RGB vector options
##################
These options are applied to 'rgbvector' overlays.
-in {none,linear,spline,true_spline}, --interpolation {none,linear,spline,true_spline}
Interpolation
-u, --unitLengh Alias for --normaliseColour.
-cm CMAP, --cmap CMAP
Colour map (only used if a colour image is provided)
-or LO HI, --colourRange LO HI
Colour-by range (only used if a colour image is
provided)
-mr LO HI, --modulateRange LO HI
Modulation range (only used if a modulation image is
provided)
-mm {brightness,alpha}, --modulateMode {brightness,alpha}
Modulate vector 'brightness' (default) or 'alpha'
-cr LO HI, --clippingRange LO HI
Clipping range (only used if a clipping image is
provided)
-xc R G B, --xColour R G B
X colour (0-1)
-yc R G B, --yColour R G B
Y colour (0-1)
-zc R G B, --zColour R G B
Z colour (0-1)
-xs, --suppressX Suppress X magnitude
-ys, --suppressY Suppress Y magnitude
-zs, --suppressZ Suppress Z magnitude
-sm {white,black,transparent}, --suppressMode {white,black,transparent}
Replace suppressed colours with 'white' (default),
'black', or 'transparent'.
-nr, --normaliseColour
Normalise RGB values to uniform brigntness.
-co FILE, --colourImage FILE
Image to colour vectors with
-mo FILE, --modulateImage FILE
Image to modulate vector brightness/alpha with
-cl FILE, --clipImage FILE
Image to clip vectors with
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
##############
Tensor options
##############
These options are applied to 'tensor' overlays.
-dl, --disableLighting
Disable lighting effect
-of, --orientFlip Flip L/R orientation within each voxel. Default: true
for images with neurological storage order, false for
images with radiological storage order. Passing this
flag will invert the default behaviour.
-tr INT, --tensorResolution INT
Tensor resolution/quality (4-20, default: 10)
-s PERC, --scale PERC
Tensor size (percentage of voxel size; 50-600,
default: 100)
-cm CMAP, --cmap CMAP
Colour map (only used if a colour image is provided)
-or LO HI, --colourRange LO HI
Colour-by range (only used if a colour image is
provided)
-mr LO HI, --modulateRange LO HI
Modulation range (only used if a modulation image is
provided)
-mm {brightness,alpha}, --modulateMode {brightness,alpha}
Modulate vector 'brightness' (default) or 'alpha'
-cr LO HI, --clippingRange LO HI
Clipping range (only used if a clipping image is
provided)
-xc R G B, --xColour R G B
X colour (0-1)
-yc R G B, --yColour R G B
Y colour (0-1)
-zc R G B, --zColour R G B
Z colour (0-1)
-xs, --suppressX Suppress X magnitude
-ys, --suppressY Suppress Y magnitude
-zs, --suppressZ Suppress Z magnitude
-sm {white,black,transparent}, --suppressMode {white,black,transparent}
Replace suppressed colours with 'white' (default),
'black', or 'transparent'.
-nr, --normaliseColour
Normalise RGB values to uniform brigntness.
-co FILE, --colourImage FILE
Image to colour vectors with
-mo FILE, --modulateImage FILE
Image to modulate vector brightness/alpha with
-cl FILE, --clipImage FILE
Image to clip vectors with
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
##########
SH options
##########
These options are applied to 'sh' overlays.
-of, --orientFlip Flip L/R orientation within each voxel. Default: true
for images with neurological storage order, false for
images with radiological storage order. Passing this
flag will invert the default behaviour.
-sr INT, --shResolution INT
FOD resolution/quality (3-10, default: 5)
-so ORDER, --shOrder ORDER
Maximum SH function order (0-maximum determined from
image [up to 16], default: maximum)
-s PERC, --size PERC FOD size (10-500, default: 100)
-no, --normalise Normalise FOD sizes
-l, --lighting Enable dodgy lighting effect
-t REAL, --radiusThreshold REAL
Hide FODs with radius less than this (min: 0, max: 1,
default: 0.05)
-m {direction,radius}, --colourMode {direction,radius}
Colour by 'direction' or 'radius' (default: direction)
-cm CMAP, --cmap CMAP
Colour map (only used if a colour image is provided)
-or LO HI, --colourRange LO HI
Colour-by range (only used if a colour image is
provided)
-mr LO HI, --modulateRange LO HI
Modulation range (only used if a modulation image is
provided)
-mm {brightness,alpha}, --modulateMode {brightness,alpha}
Modulate vector 'brightness' (default) or 'alpha'
-cr LO HI, --clippingRange LO HI
Clipping range (only used if a clipping image is
provided)
-xc R G B, --xColour R G B
X colour, if colouring by 'direction'
-yc R G B, --yColour R G B
Y colour, if colouring by 'direction'
-zc R G B, --zColour R G B
Z colour, if colouring by 'direction'
-xs, --suppressX Suppress X magnitude
-ys, --suppressY Suppress Y magnitude
-zs, --suppressZ Suppress Z magnitude
-sm {white,black,transparent}, --suppressMode {white,black,transparent}
Replace suppressed colours with 'white' (default),
'black', or 'transparent'.
-nr, --normaliseColour
Normalise RGB values to uniform brigntness.
-co FILE, --colourImage FILE
Image to colour vectors with
-mo FILE, --modulateImage FILE
Image to modulate vector brightness/alpha with
-cl FILE, --clipImage FILE
Image to clip vectors with
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
Available colour maps: blue, blue-lightblue, brain_colours_1hot,
brain_colours_1hot_iso, brain_colours_2winter, brain_colours_2winter_iso,
brain_colours_3warm, brain_colours_3warm_iso, brain_colours_4cool,
brain_colours_4cool_iso, brain_colours_5redyell, brain_colours_5redyell_iso,
brain_colours_6bluegrn, brain_colours_6bluegrn_iso, brain_colours_actc,
brain_colours_actc_iso, brain_colours_blackbdy, brain_colours_blackbdy_iso,
brain_colours_bluegray, brain_colours_bluegray_iso, brain_colours_bone,
brain_colours_bone_iso, brain_colours_cardiac, brain_colours_cardiac_iso,
brain_colours_cortex, brain_colours_cortex_iso, brain_colours_diverging_bgy,
brain_colours_diverging_bgy_iso, brain_colours_diverging_bwr,
brain_colours_diverging_bwr_iso, brain_colours_flow, brain_colours_flow_iso,
brain_colours_french, brain_colours_french_iso, brain_colours_ge_color,
brain_colours_ge_color_iso, brain_colours_gold, brain_colours_gold_iso,
brain_colours_gooch, brain_colours_gooch_iso, brain_colours_greengray,
brain_colours_greengray_iso, brain_colours_hotiron, brain_colours_hotiron_iso,
brain_colours_nih, brain_colours_nih_fire, brain_colours_nih_fire_iso,
brain_colours_nih_ice, brain_colours_nih_ice_iso, brain_colours_nih_iso,
brain_colours_nih_new, brain_colours_nih_new_iso, brain_colours_pink,
brain_colours_pink_iso, brain_colours_rainramp, brain_colours_rainramp_iso,
brain_colours_redgray, brain_colours_redgray_iso, brain_colours_spectrum,
brain_colours_spectrum_iso, brain_colours_surface, brain_colours_surface_iso,
brain_colours_x_hot, brain_colours_x_hot_iso, brain_colours_x_rain,
brain_colours_x_rain_iso, cool, copper, cortical, green, greyscale, hot, hsv,
pink, random, red, red-yellow, render1, render1t, render2, render2t, render3,
retino, subcortical, yellow. You can also specify any matplotlib colour map,
or a colour map file.
###########
MIP options
###########
These options are applied to 'mip' overlays.
-ll, --unlinkLowRanges
Unlink low display/clipping ranges
-lh, --linkHighRanges
Link high display/clipping ranges
-dr LO HI, --displayRange LO HI
Display range. Setting this will override
brightnes/contrast settings. For volume overlays only:
append a "%" to the high value to set range by
percentile.
-cr LO HI, --clippingRange LO HI
Clipping range. Setting this will override the low
display range (unless low ranges are unlinked). For
volume overlays only: append a "%" to the high value
to clip by percentile.
-g REAL, --gamma REAL
Gamma correction [-1-+1, default: 0]
-ic, --invertClipping
Invert clipping
-cm CMAP, --cmap CMAP
Colour map
-cmr INT, --cmapResolution INT
Colour map resolution
-in {none,linear,spline,true_spline}, --interpolation {none,linear,spline,true_spline}
Interpolation
-inc, --interpolateCmaps
Interpolate between colours in colour maps
-i, --invert Invert colour map
-w PERC, --window PERC
Length of the window along which the MIP is
calculated. Specified as a proportion of the image
length. The window is centred at the current display
location.
-m, --minimum Use the minimum intensity, rather than the maximum
intensity, in the projection.
-ab, --absolute Use the absolute intensity, rather than the maximum
intensity, in the projection. This overrides the
minimum intensity setting.
-v INT, --volume INT Volume (index, starting from 0).
-x IDX4,IDX5,..., --index IDX4,IDX5,...
Index into each dimension, for images with more than
four dimensions, Specify as a comma-separated list of
indices (starting from 0), where the first value is
the index into the fourth dimension.
##################
Tractogram options
##################
These options are applied to 'tractogram' overlays.
-cs {affine,pixdim,pixdim-flip,id,torig}, --coordSpace {affine,pixdim,pixdim-flip,id,torig}
Overlay vertex coordinate space (relative to reference
image)
-lw REAL, --lineWidth REAL
Streamline width/diameter
-sw PERC, --sliceWidth PERC
2D only. Slice width when drawing 2D slices.
-r INT, --resolution INT
Streamline resolution/quality
-s PERC, --subsample PERC
Draw a randomly selected subsample of streamlines.
-p, --pseudo3D 2D only. Draw the full 3D tractogram, overlaid on the
2D scene. The default behaviour is to draw a cross-
section of the tractogram at the current depth.
-xcl {low,high,slice,none}, --xclipdir {low,high,slice,none}
2D only. Direction in which to clip (hide) areas
below/above the current X location.
-ycl {low,high,slice,none}, --yclipdir {low,high,slice,none}
2D only. Direction in which to clip (hide) areas
below/above the current Y location.
-zcl {low,high,slice,none}, --zclipdir {low,high,slice,none}
2D only. Direction in which to clip (hide) areas
below/above the current Z location.
-ll, --unlinkLowRanges
Unlink low display/clipping ranges
-lh, --linkHighRanges
Link high display/clipping ranges
-un, --useNegativeCmap
Use negative colour map (automatically enabled if
--negativeCmap is specified)
-dr LO HI, --displayRange LO HI
Display range. Setting this will override
brightnes/contrast settings. For volume overlays only:
append a "%" to the high value to set range by
percentile.
-cr LO HI, --clippingRange LO HI
Clipping range. Setting this will override the low
display range (unless low ranges are unlinked). For
volume overlays only: append a "%" to the high value
to clip by percentile.
-mr LO HI, --modulateRange LO HI
Modulate range. Sets the range by which opacity should
be modulated by. For volume overlays only: append a
"%" to the high value to modulate by percentile.
-g REAL, --gamma REAL
Gamma correction [-1-+1, default: 0]
-ls, --logScale Logarithmic scaling
-ic, --invertClipping
Invert clipping
-cm CMAP, --cmap CMAP
Colour map
-nc CMAP, --negativeCmap CMAP
Colour map for negative values
-cmr INT, --cmapResolution INT
Colour map resolution
-inc, --interpolateCmaps
Interpolate between colours in colour maps
-i, --invert Invert colour map
-ma, --modulateAlpha Modulate alpha by intensity
-ima, --invertModulateAlpha
no help
-xc R G B, --xColour R G B
X colour (0-1)
-yc R G B, --yColour R G B
Y colour (0-1)
-zc R G B, --zColour R G B
Z colour (0-1)
-xs, --suppressX Suppress X magnitude
-ys, --suppressY Suppress Y magnitude
-zs, --suppressZ Suppress Z magnitude
-sm {white,black,transparent}, --suppressMode {white,black,transparent}
Replace suppressed colours with 'white' (default),
'black', or 'transparent'.
-nr, --normaliseColour
Normalise RGB values to uniform brigntness.
-ri FILE, --refImage FILE
Reference image for overlay
-co FILE, --colourBy FILE
NIFTI image, or file containing per-vertex/streamline
scalar values for colouring, or name of a a per-
vertex/streamline data set contained within the
tractogram file.
-cl FILE, --clipBy FILE
NIFTI image, or file containing per-vertex/streamline
scalar values for clipping, or name of a a per-
vertex/streamline data set contained within the
tractogram file.