Anatomist user manual¶
Anatomist software enables objects visualization and handling for medical imaging. These objects are various representations of anatomical and functional information coming from images (T1 MRI, activation image issued from a parametrical statistical map, PET, hemispheres mesh, fibers bundles obtained from BrainVISA tracking process, sulci graph representation extracted from a T1 MRI image…).
Features and originality of Anatomist are based on:
Management of several types of objects: structured (sulci, ROI graphs…) or not (3D, 4D volumes, mesh …)
Management of coordinate systems and transformations, for instance, you can load transformation matrix to change the object coordinate systems. For example, it is possible to merge a non normalized anatomical volume and a normalized activation map (functional data), and to have a coherent display if we load the transformation from the normalized image to the non normalized anatomical image or the reverse.
Possibility of building complex 3D scenes with several objects of any type (merging, superimposing…).
A lot of tools: color palettes, region of interest module, mathematic morphology, manual registration (transformation control) …
Anatomist control window (main window) enables to have a general view of loaded objects and opened windows, to choose actions for combining objects (merging…), or controls to use on windows according to contained objects. Here’s Anatomist control window:
The general purpose is to load objects (volume, ROI graph, mesh…), change their referential (coordinate system) if needed, modify their characteristics, combining them (merging, superimposing…), and put them in windows in order to visualize them.
So, here are some base principles for using Anatomist:
Load objects that represent volumes, meshes …
These objects are put in windows for visualization. At a more advanced level of use, it is possible to put several objects in the same windows, for example to superimpose a mesh and a volume.
It is also possible to handle objects characteristics as referential (coordinate system) or colors, for example by modifying a volume’s palette.
A window offers different control modes according to the type of its contained objects. For example, if a window contains a ROI graph, the selection control will be available and will enable to select regions in the graph.
Here are some examples about typical actions in Anatomist, for example to look at a volume:
Install and start Anatomist software¶
Download: see the BrainVISA web site download page
See also the Anatomist tutorial
And the BrainVISA installation section
When starting to use Anatomist, you may need to configure some options. The most important is to choose (or to check if several users share the same Anatomist configuration) how to display axial and coronal views: either in radiological convention or in neurological convention.
To go to preferences pannel, click on Settings and on Preferences. Let’s see the different tabs:
Language: default (system language) / en (english) / fr (french).
HTML browser command line: the browser that will be used to see HTML documentation (firefox / konqueror …).
User level: basic, advanced or expert. Some features are available only in advanced or expert mode, for example flight simulator control and storage to memory transformation automatic loading.
Default referentials: this advanced option enables to choose a default referential for loaded object and for new windows independently. By clicking on the grey button, you can choose them with:
Linked cursor tab¶
Display linked cursor: if enabled, a symbol is displayed to represent the linked cursor position when you click on a window.
Cursor shape: several shapes are available (arrow, cross, multicross …). It is also possible to load a cursor (regular Anatomist object).
Size: set cursor size.
Cursor color: default color is red. You can choose another color.
Axial/coronal slices orientation: selection of images display convention.
Default windows size: windows zoom factor, by default the value is 1 for a volume whose voxels size is (1x1x1). So on screen, a pixel size is 1mm.
Control window tab¶
Display nice logo: enable displaying of Anatomist logo on top of the main window.
Interpolation on volumes when changing referential: on loading a referential for an image (applying a transformation) or during a fusion, the volume is resampled by a trilinear interpolation or by the closest sibling value.
Use referential / transformations information found in objects headers (SPM, NIFTI…): if a loaded image has spm_origin, transformations, or referentials attributes in its header, it is possible to automatically load the corresponding referentials and transformations in Anatomist. See Loading referential information to know more about this feature.
Assume all “scanner-based” referentials are the same: by default they are considered all different.
To keep these preferences for further sessions, you must save them:
If the configuration file is shared between several users, make sure that you all use the same preferences and regularly check that your parameters haven’t been changed. Indeed, if a user modifies a parameter like the display convention (neurological or radiological), images display will change. Configuration is shared if you are identified as the same user.
You can start Anatomist with a customized configuration even if you share the same user with other people. To use a particular profile, start Anatomist with a profile name (even if it doesn’t exists yet). For example:
anatomist -u toto
and then save preferences to keep them for a further session.
Every profile has its own configuration directory, which is localized according to the system (user is the login used to connect to the computer, it can be for example your name):
C:\Documents and Settings\user\.anatomist-toto\
To start Anatomist with this profile:
anatomist -u toto
Configuration file and options¶
The configuration file format and options is decribed in this document
A window enables to visualize one or several objects. These objects can have the same type (e.g.: 2 meshes for the brain hemispheres) or different types (e.g.: a mesh and a volume). Windows have a name, for example
A(2):anat.vimg. This name means that the window is the second axial window and contains the volume
anat.vimg. It is possible to handle windows individually or in groups.
There are several ways to open a window:
Menu Windows => <window type>
Click on window type icon
When using Anatomist intensively, users often get entangled in several dozens of Anatomist windows. Windows titles and numbering is often not enough to distinguish them in the main control window and on the desktop. To help finding out the correspondance between windows listed in the control window and the actual displayed ones, there are some hints:
Moving the mouse cursor over a window name in the main control window should highlight the corresponding view (in light blue). (this feature appeared in Anatomist 4.3).
In the same way, when dragging objects onto windows in the control window, the target window(s) will also highlight in light blue.
double-clicking on a window in the list will make the corresponding window to get displayed on top, and to un-iconify if it was iconified or hidden.
Windows enable to visualize objects after their loading. Note that visualization is different from loading. Indeed, loading gives raw data that can be visualized in various way. For example, you can change the display convention without modifying the data. See Load and display objects for more details.
The table below shows the different window types.
2D Axial window - Visualization of volumes.
2D Coronal window - Visualization of volumes.
2D Sagittal window - Visualization of volumes.
3D window - Visualization of 2D objects and 3D objects (for example meshes).
Browser - Visualization of object attributes, window content or structured objects.
Profile - Visualization of grey levels range along an axis.
Histogram - Visualization of grey levels histogram.
Additional windows types may be provided in plugins.
2D and 3D windows are actually different modes of the same window type: you can switch from one type to another by clicking on the icons on window’s top bar.
This type of window enables to see an oblique slice and buckets (set of voxels), that are displayed differently in 2D and in 3D. This window enables to keep the slice orientation as if you were in a 3D window but to display buckets as if you were in a 2D window.
The following images show the difference between 3D, 2D and oblique windows for MRI and ROI visualization:
Histogram, Profile, and Matplotlib-based variants¶
The “older” Profile and Histogram windows were somewat limited: interactions were not really allowed on these kind of windows. Moreover, coordinates transformations were not properly handled in Profile windows.
Newer modules, programmed in Python language, make use of the Matplotlib library and provide newer alternatives for profile and histogram fully support interactive zooming, clicking on positions, and coordinates transformations.
Windows can be grouped in order to:
Use a linked cursor specific for the group (don’t forget to enable Settings => Preferences => Linked cursor => Display linked cursor option).
Handle the same object in all windows of the group: click on View / select objects contextual menu in a window of the group, a browser appears. Select the object in the browser. Note: by default all windows are considered to be in the same group and objects can be selected in all windows via any browser window.
To create a windows group:
Select the windows to link in the windows panel (on the right). For multiple selection, press Ctrl key and click.
Then create the group with Windows => Link windows menu.
To undo a windows group:
Select the group on right panel.
Undo the group with Windows => Unlink windows
A windows block is a window that can contain several views.
Select the image you want to visualize. Open a 4 views block using the Windows => Open a 4 views block menu.
You can add a new window to the block by dragging the window item from Anatomist’s list of windows and dropping it in the block.
To remove a window from the block, use the window menu Window => Detach view.
It is also possible to reorganize the block by changing the views layout, using the options in the block window menu.
Objects handled by Anatomist¶
Object stands for all type of data that Anatomist can handle. This software manages volumes (T1, fMRI, …), meshes, textures (to stick on other objects), structured objects like sulci graphs or ROI graphs. All these objects can be visualized and combined (merging, superimposing…). Some data types and formats are peculiar to Anatomist, like for example meshes (.mesh or .tri), or nomenclature (.hie).
Main objects handled by Anatomist are listed below (the list is not exhaustive because there are also merged objects, volume slices…):
|Icon||Anatomist data type||Description and Format / Extension|
|2D, 3D and 4D volume.||
Formats list, non exhaustive, according to the operating system ad installed plugins:
Script to execute a sequence of actions. For example, a script can be a file containing commands to merge two volumes and load a specific palette.
Format: Anatomist history file: .ana
A bucket is a set of points coprresponding for example to a region of interest, ie a voxels list (it is not possible to see the coordinates, only display is managed).
Surfacic meshes ( 3D mesh of hemispheres, brain, cortex...). Polygons may be triangles, or segments (wireframe) but all formats do not support them.
A texture is a list of values mapping on a mesh. Or a time-series of values.
|Textured Mesh ("TEXTURED SURF.")||
Textured surfaces can be saved since Anatomist 4.5. Actually several types of textured meshes (fusion 3D for instane) may be savec this way, but reloading them will load a "standard" textured surface, so dynamical aspects of the object will be lost.
|FUSION2D Object||Object created by merging objects with Fusion2D method (for example: merging two volumes).|
|FUSION3D Object||Object created by merging objects with Fusion3D method (for example: merging a volume and a mesh). Texture file, containing data to stick on meshes.|
|CutMesh object||Object created by merging objects with CutMesh method (for example: merging a volume and a mesh).|
|Volume Rendering Fusion||See Volume rendering.|
|PlanarFusion3D object||Object (textured plane) obtained by merging a mesh slice plan (Planar mesh) and a volume. For example, in a FusionCutMeshMethod fusion between a volume and a mesh, PlanarFusion3D object will be the textured plan of the volume according to the slice plan of the mesh.|
Structured container objects
Bundles are sets of fibers obtained from diffusion MRI imageng by a fiber tracking algorithm. They are loaded in Anatomist as graphs.
Loading an object¶
There are several ways to load an object in Anatomist:
Click on menu File => Open and then choose the file to load with the file browser.
Click on Open button in the main window.
Drag and drop a file in Anatomist from a file explorer or from brainvisa database browser.
The loaded files appear in Anatomist main window’s left panel.
It is also possible to drag and drop an object from Anatomist to a console or a file explorer in order to copy the file or the filename.
Most objects are described by common attributes that give information about them. For example, a volume has attributes for voxels size, image size… Each object can also have specific attributes. To see these attributes, you can put the object in a browser .
Putting an object in a browser does not always enable to see its attributes, it depends on the type of the object. Indeed, a browser also enables to see the structure of complex objects, like graph nodes.
Some attributes may be loaded with the object, and induce specific interpretation by Anatomist, like colors. See Objects properties used at load time for a description of it.
There are several ways of visualizing an object in a window (after object loading):
Drag and drop the object on a window icon of the left menu bar (it will open a new window containing this object).
Drag and drop the object on an already opened window.
Drag and drop the object on an opened window icon in the right panel.
Select the object and a window and click on add button in the left menu bar.
Select the object and a window and click on Objects => Add objects in windows menu.
Likewise, there are several ways to remove an object from a window:
Select the object and the window and click on Remove button in the left menu bar.
Select the object and the window and click on Objects => Remove objects from windows menu.
Copying Objects from one window to another¶
It is possible to copy all objects from a window to another window: drag and drop any point of the source window border in the destination window. This will open all visible objects of the source window in the destination window.
Press the CTRL key during the drag and drop if you want to copy only the currently selected objects of the source window.
What is a control ?¶
A control defines the way mouse and keyboard act on a window or an object. It can also be associated to a toolbox (regions of interest drawing for example). According to the type of objects contained in the window, some action modes can be disabled. For example, the selection mode has no effect on a volume because there are no areas to select on a volume. But you can select areas in a ROI graph (graph nodes).
Some controls are available only on selected objects. You can select objects in a window via the right click menu view / select objects.
Description : Default control enables to use the linked cursor, to zoom in, to rotate…
Camera: rotation, zoom, translation¶
Fullscreen, hiding tools and menu…
removing objects: DEL key
Slices and time handling¶
Description : Select objects and graph nodes, rotate…
The selection control allows to “select” objects in Anatomist windows by clicking on them in 3D views. Selected objects become highlighted, and can then be used for specific operations.
The default highlighting of selected object changes their color in 3D visualizations, using a red color (by default), and displays a bounding box wireframe around selected objects. Alternative selection highlighting can be chosen, either in the “graph parameters” windows (accessed via the menus of the main window), or via extension modules, in a specific tools panel in the controls parameters box (accessed via the F1 key in 3D views), in the “selection” tab. Highlighting can then be displayed by outlining selected objects, an/or by drawing a parallelepipedic box around seleced objects.
When selecting graph nodes, specific options can decide whether to also show graph relations attached to selected nodes. These are controlled in the selection tab of the controls tools window. In “Basic” mode, relations are not handled by the selection control. In “Intersection” mode, relations linking selected nodes are displayed. In “Union” mode, relations attached to any of the selected nodes are displayed. This graph relations display mode can be useful for complex graphs carrying multimodal structural relational data, such as fibers connecting cortical regions.
Labels copy/paste tool¶
The selection control also brings access to a ROI and sulci renaming tool: labels can be picked on a selected graph node, using the space key, and pasted onto other selected nodes, using the ctrl + Return key combination. It is possible to pick a label from one graph / window, and to paste it into another graph / window, provided both winfdows are not in different groups (like the selection, labels copy/paste works by windows group). The current label which has been copied is visible on the top toolbar of wnidows in selection mode.
This tool is especially useful to work with cortical sulci, typically to fix automatic sulci identifications.
Remember that graphs (sulci graphs especially) may use 2 attributes for labels: “label” or “name”, typically meaning automatic or manual identification. The label copy/paste tool will use the currently selected mode.
Graph labels display as text¶
The A key activates (or desactivates) a “graph annotation” mode, which displays the labels of the regions in a graph as text in 3D.
Oblique view control¶
Description : Creates oblique view by rotating the slice plan.
Flight simulator control¶
Description : Available in expert mode only. It enables to change the point of vue with the keyboard.
Description : Enables to move an object in a view in order to make manual registration. It can be useful to initialize a registration method with translation parameters. You can get theses parameters in the .trm file obtained from this registration. See the part manual registration for more details.
Hand-drawing of Regions of Interest (ROI)¶
Description : See the part ROI drawing toolbox for more details.
Threshold ROI drawing mode under connectivity to clicked point constraint¶
Description : Opens the ROI toolbox. Use the Connectivity threshold tab to define min and max bounds for the voxels to select.
ROI design by discriminating analysis¶
Description : Opens the ROI toolbox. Use the DynSegment tab to fix parameters. This is usable on dynamic data only.
ROI drawing mode by label selection¶
Description : selects region according to their labels.
Surface paint control¶
Description : This control appears when a mesh is opened in a 3D window using the button in Anatomist main window. It is available when the mesh object is selected. See the part about the Surface paint module for more details.
In addition to the standard rotation, zoom and translation actions, a few specitic actions are found:
the left mouse button is linked to the current selected SurfPaint tool
The right mouse button closes a started path (instead of the usual popup menu)
Undo and redo actions
Validate (return) or cancel (esc) the currently started compound action (path, fill etc)
Possibility to quiclky interact with the slice and clipping plane, using Ctrl-I to invert the plane, and Shift/Ctrl + right mouse button to rotate the plane. This functionality is especially useful when dealing with very convoluted surfaces.
Mesh cutting control¶
Description : available only if a cut mesh is selected (cut mesh is obtained by fusion between a mesh and a volume). It controls the slice on a cut mesh.
Fold split control¶
This specialized control allows to manually cut a sulci graph node into several parts. It can be done by selecting a single point (by clicking on a sulcus node at the desired position), or by selected several points which will be linked to form a cut line: Ctrl + left click sets points (the order is important), then the S key proposes a split line joining the selected points. When a split line (purple voxels line) is proposed, the user can validate and actually split by hitting (or re-hitting) the S key. Actions can be aborted before the split is actually done, by hitting the ESC key.
A more automatic mode allows to automatically subdivize large nodes: clicking on a node with Ctrl + right click will subdivize a single node.
Shift + right click on any node of a graph will apply the automatic subdivizion of all large nodes of a graph.
Note that after splitting, nodes are not automatically remeshed, graph relations have been altered, and all morphometric measurements on altered nodes are out of date. To be usable for sulci recognition and morphometry, the graph should go through an update process, which is available in BrainVISA.
Anatomist user manual (2)¶
This document is continued here: