Anatomist: Configuration options

Anatomist can be customized in a personal options file. This file is located in the .anatomist/config directory of your account and is named settings.cfg (${HOME}/.anatomist/config/settings.cfg on unix).
The configuration file holds the settings selected from the Preferences menu of Anatomist, and may contain additional, "hidden" options which are not (or not yet) accessible via the user interface. It is basicly a list of options with values and the file can have two distinct formats at the moment.

  • "Tree" format looks like the following: 
    *BEGIN TREE anatomist_settings
anatomist_version   1.30alpha
enableUnstable      1
html_browser        konqueror %1 &
*END
  • "Python" format looks like this: 
    attributes = {
    '__syntax__' : 'anatomist_settings',
    'anatomist_version' : '1.30alpha',
    'enableUnstable' : 1,
    'html_browser' : 'konqueror %1 &',
  }
  • In the future this file will move to XML format, but this is only the future.

    • Python format is more flexible than the older "tree" format because it allows unknown tags. This is important because it keeps compatibility with older anatomist versions: at the moment, new options saved in thge settings file will prevent older anatomist versions to read the whole file. Inversely, the python format is only supported (and readable) since Anatomist 1.29.

    Options value can take simple types: string, int, float, vector of int...

    Here is a complete (I hope) list of the possible options:

    Option Type Default value Possible values Description Exists since anatomist version
    anatomist_version string Higher version used all
    axialConvention string radio radio, neuro Display convention for axial and coronal slices 1.30
    controlWindowLogo int 1 0, 1 Allows to hide the logo image and (take less space) all
    cursorColor int_vector None RGB (3 ints) Color of the 3D windows cursor. Only valid if cursorColorAuto is 0 all
    cursorColorAuto int 1 0, 1 In auto mode, a default color is taken and cursorColor is not taken into account all
    cursorShape string cross cross, circle Shape of the 3D cursor. In Anatomist 1.30, only cross was implemented. In Anatomist 3.0, cursors can be any anatomist object. A number of cursors are available, and users can add their own ones in their .anatomist/cursors directory. all
    cursorSize int 20 Size of the 3D cursor (in mm) all
    enableUnstable int 0 0, 1 Enable or disable unstable and buggy (dangerous) features 1.30
    graphDisplayMode string meshes meshes, voxels, all, first Display mode for 3D objects in graph nodes and relations all (used since 3.0)
    graphHierarchyAttribute string name name, label Graph nodes attribute used to link and color with nomenclature names all (used since 3.0)
    graphUseHierarchy int 1 0, 1 enable or disable the coloring of graph 3D elements according to a nomenclature hierarchy all (used since 3.0)
    graphUseToolTips int 1 0, 1 enable or disable tooltips on 3D views, to display graph nodes labels all (used since 3.0)
    html_browser string system dependent command used to run a HTML borwser for the documentation all
    language string system default en, fr, ... Translation language in the GUI all
    leftRightDisplayed int unused yet all
    linkedCursor int 1 0, 1 Display / hide the 3D cursor all
    listview_background string None Image file to be displayed in "listview" widgets of the GUI: the control window objects and windows lists, browsers etc. This is only a gadget to customize the look of Anatomist. Filenames without an absolute path are taken in the ${HOME}/.anatomist/icons/ directory all
    path_list string Paths list to be inserted in the pre-seelcted directories of file dialogs. It can be useful to reach quickly your favorite data directories all
    selectionColor int_vector RGB (3 ints) Selection color for graph nodes all
    selectionColorInverse int 0 0, 1 If this option is enabled, the selection color is the negative of the original color of the selected object. In this case, selectionColor is not taken into account all
    useSpmOrigin int 0 0, 1 If enabled, SPM volumes with an origin are automatically assigned a referential and transformation at load time to take it into account. This used to be the default and only possible behaviour in anatomist 1.29 and previous versions, but as it is often annoying, it has been disabled. When disabled, the same referential can be created via an object-specific option of volumes 1.30
    volumeInterpolation int 1 0, 1 By default, resampled volumes values are interpolated from neighbouring voxels. This gives a nice smooth aspect but is slower and may not let you see the exact limits of the voxels. all
    windowSizeFactor float 1.0 > 0 Default windows size factor. 1.0 corresponds to 1 pixel for 1mm in data space, larger values means larger windows. Depending on the size and resolution of your screen, you may want to change this default value. 3.0