Commit 19a0ee63 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

DOC: tractodoc

parent 740dcb43
......@@ -23,6 +23,13 @@ the *Views* |right_arrow| *3D view* menu item.
:align: center
In the 3D view, the order of overlays in the :ref:`overlay list
<ortho_lightbox_views_overlay_list>` does not have any effect on the display -
instead, all compatible overlays that you have loaded will be drawn and
blended into a single scene, based on their locations in the :ref:`world
coordinate system <display_space_world_space>`.
.. note:: 3D visualisation functionality and quality will vary, depending on
how you are running FSLeyes, For example, if you are running
FSLeyes over a remote SSH/X11 session, quality will be lower, and
......@@ -59,6 +66,8 @@ streamline tractograms. As with the :ref:`ortho and lightbox views
on the |gear_icon| button.
.. _3d_view_volume:
Volume overlays
^^^^^^^^^^^^^^^
......@@ -88,18 +97,18 @@ The following settings can be used to control the ray-casting:
- **Blend by intensity** By default, areas of the image with lower voxel
intensities will be made more transparent. This setting allows that
behaviour to be disabled.
behaviour to be disabled. When you disable this option, you can use
the **Clipping range** sliders to hide background/low-intensity voxels.
- **Number of samples** This setting controls how many samples are taken
through the volume. A higher number of samples will result in a better
quality rendering.
- **Quality** This setting controls the resolution of the final rendering.
Setting it to 100% will render the result at the display
resolution. Reducing this setting will improve the rendering speed - a
useful strategy is to reduce the quality, experiment with the other display
settings until you are happy, and then increase the quality for the final
rendering.
Setting it to 100% will render the result at the display resolution.
Reducing this setting will improve the rendering speed - a useful strategy
is to reduce the quality, experiment with the other display settings until
you are happy, and then increase the quality for the final rendering.
Volume clipping
......@@ -140,6 +149,8 @@ settings allow you to control each clipping plane:
rotation of the plane with respect to a horizontal plane.
.. _3d_view_mesh:
Mesh overlays
^^^^^^^^^^^^^
......@@ -151,15 +162,16 @@ Mesh overlays
The 3D display settings for mesh overlays are much the same as the :ref:`2D
display settings <overlays_mesh>`. You can choose different variants of the
same mesh via the **Surface definition** setting, and you can display data on
the surface via the **Vertex data** setting.
same mesh (e.g. wm, pial, midthickness) via the **Surface definition**
setting, and you can display data on the surface via the **Vertex data**
setting.
The default behaviour, when you are colouring a mesh with some vertex data, is
for the colours to be interpolated (smoothed) across the mesh
surface. However, if you are viewing discrete data (e.g. anatomical labels),
and/or wish to display the mesh with flat, unsmoothed colours, you change the
**Interpolation** option to **Nearest**.
and/or wish to display the mesh with flat, unsmoothed colours, you may change
the **Interpolation** option to **Nearest**.
.. _3d_view_tractogram:
......@@ -168,62 +180,33 @@ Tractogram overlays
^^^^^^^^^^^^^^^^^^^
.. image:: images/3d_view_tractogram_blended.png
:width: 30%
:align: left
All of the options for displaying :ref:`tractograms <overlays_tractogram>` are
available in the 3D view. In a 3D view, each streamline is drawn as a line or
cylinder.
FSLeyes can display `TrackVis <http://trackvis.org/>`_ ``.trk`` and `MRtrix3
<https://www.mrtrix.org/>`_ ``.tck`` streamline tractography (*tractogram*)
data sets.
.. container:: image-strip
.. image:: images/3d_view_tractogram_blended.png
:width: 25%
The overlay display settings dialog (the |gear_icon| button) has several
options allowing you to control how tractograms are displayed.
.. image:: images/3d_view_tractogram_orientation.png
:width: 25%
.. image:: images/3d_view_tractogram_density.png
:width: 25%
The **Streamline width** option controls the thickness of each streamline.
The **Streamline resolution** option allows you to control whether streamlines
are drawn as lines (lower resolution), or as tubes (higher resolution) - when
you increase the streamline resolution, a lighting effect will be applied to
the streamlines. Lighting can be disabled in the view settings dialog (the
|spanner_icon| button).
The **Colour streamlines by** option allows you to control how a tractogram
is coloured. Streamlines can be coloured in one of three ways - the default
setting is to colour them according to their XYZ orientation. The colours
that correspond to each of the XYZ directions can be changed, in the same
manner as for :ref:`vector images <overlays_vector>`.
.. image:: images/3d_view_tractogram_orientation.png
:width: 30%
:align: right
Streamlines can also be coloured by per-vertex/per-streamline data sets,
either stored in the tractogram file itself, or loaded from a separate data
file (click on the **Load vertex data** button can to load data from a
separate file). Finally, streamlines can be coloured by the values in a
separate NIfTI image.
When colouring streamlines according to a data set or image, the :ref:`usual
options <overlays_volume>` are available to control colouring, including
choosing a **Colour map**, controlling the **Display range**, and modulating
transparency by the data.
.. image:: images/3d_view_tractogram_density.png
:width: 30%
:align: left
|
The **Clip streamlines by** option can be set independently of the **Colour
streamlines by** option, and can be used to clip/hide streamlines according to
the data set, and **Clipping range** that you specify.
In the 3D view, the **Width** option controls the thickness of each
streamline. The **Resolution** option allows you to control whether
streamlines are drawn as lines (lower resolution), or as cylinders (higher
resolution) - when you increase the streamline resolution, a lighting effect
will be applied to the streamlines. Lighting can be disabled in the view
settings dialog (the |spanner_icon| button).
Finally, it is worth playing with the **Opacity** setting, as some nice
visualisation effects can be achieved.
It is worth playing with the **Opacity** setting, as some nice visualisation
effects can be achieved.
......@@ -242,7 +242,7 @@ Volume
This is the default (and most conventional) display type for NIFTI
images. Voxel intensities are coloured according to a colour map. The display
range used to colour voxels can be adjusted, and voxels can be *clipped*
(hidden) with an independent clipping range.
(hidden) with an independent clipping range [*]_.
.. container:: image-strip
......@@ -260,6 +260,10 @@ range used to colour voxels can be adjusted, and voxels can be *clipped*
|
.. [*] See :ref:`here <3d_view_volume>` for details on viewing volumes in
the 3D view.
The following settings are available for volume overlays:
......@@ -838,8 +842,8 @@ on diffusion SH overlays:
magnitude of their radii.
.. [*] The FOD lighting model in FSLeyes |version| is broken, as I have not
yet figured out a way to make a better lighting model work in a
.. [*] The FOD lighting model in FSLeyes |version| is quite poor, as I have
not yet figured out a way to make a better lighting model work in a
computationally efficient manner.
......@@ -887,7 +891,8 @@ Mesh
^^^^
FSLeyes is able to display 2D cross sections of 3D triangle meshes.
FSLeyes is able to display 2D cross sections of 3D triangle meshes (see
:ref:`here <3d_view_mesh>` for details on viewing volumes in the 3D view).
.. container:: image-strip
......@@ -988,7 +993,63 @@ Tractogram
^^^^^^^^^^
FSLeyes can display TrackVis ``.trk`` and MRtrix3 ``.tck`` streamline
tractography *tractogram* data sets. Tractograms can currently only be
displayed in the :ref:`3D view <3d_view>` - options controlling tractogram
visualisation are covered :ref:`here <3d_view_tractogram>`.
FSLeyes can display `TrackVis <http://trackvis.org/>`_ ``.trk`` and `MRtrix3
<https://www.mrtrix.org/>`_ ``.tck`` streamline tractography (*tractogram*)
data sets. In the ortho and lightbox views, a 2D cross-section of the
streamline vertices at the current location is displayed. Tractograms can also
be visualised in 3D - see :ref:`here <3d_view_tractogram>` for more details.
.. container:: image-strip
.. image:: images/overlays_tractogram1.png
:width: 25%
.. image:: images/overlays_tractogram2.png
:width: 25%
.. image:: images/overlays_tractogram3.png
:width: 25%
|
*Data for some of the examples above was sourced fromn the B.A.T.M.A.N. -
Basic And Advanced Tractography with MRtrix for All Neurophiles data set,
created by Marlene Tahedl and released under a CC-By Attribution 4.0
International license (DOI 10.17605/OSF.IO/FKYHT).*
The overlay display settings dialog (the |gear_icon| button) has several
options allowing you to control how tractograms are displayed.
The **Width** option controls the diameter of each streamline point. The
**Resolution** option allows you to control the quality - at lower
resolutions, points are drawn as triangles or squares, whereas at higher
resolutions they are drawn as circles.
The **Colour by** option allows you to control how a tractogram is coloured.
Streamlines can be coloured in one of three ways - the default setting is to
colour them according to their XYZ orientation. The colours that correspond
to each of the XYZ directions can be changed, in the same manner as for
:ref:`vector images <overlays_vector>`.
Streamlines can also be coloured by per-vertex/per-streamline data sets,
either stored in the tractogram file itself, or loaded from a separate data
file (click on the **Load vertex data** button to load data from a separate
file). Finally, streamlines can be coloured by the values in a separate NIfTI
image.
When colouring streamlines according to a data set or image, the :ref:`usual
options <overlays_volume>` are available to control colouring, including
choosing a **Colour map**, controlling the **Display range**, and modulating
transparency by the data.
The **Clip by** option can be set independently of the **Colour by** option,
and can be used to clip/hide streamlines according to the data set, and
**Clipping range** that you specify.
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