Markers File Format

Markers file format

Invesalius stores markers in .mkss files. [^1] These are CSV-like tabulated textfiles (strictly speaking, they are not CSV as they use tabs instead of commas to separate values). The first line of the file contains the "magick" string ##INVESALIUS3_MARKER_FILE_ immediately followed by a an integer, e.g. ##INVESALIUS3_MARKER_FILE_0. The integer is the version number for the file format. The format of the rest of the file is version-specific.

Version 0

For version 0 the second line of the file contains column names (essentially, very brief description of each of the marker attributes, like "x", "y", "z", etc.) It is followed by the marker data, one line per marker. Each line contains the following fields:
Location of the marker (in Invesalius's internal coordinates)

• x: x coordinate of the marker
• y: y coordinate of the marker
• z: z coordinate of the marker

Three Euler angles (in degrees) specifying the marker orientation

• alpha
• beta
• gamma

Marker color in rgb format, scaled between 0 and 1

• r
• g
• b

--

• size: marker size (integer)
• label: a user-editable string describing the marker

Coordinates of a seed (used for tractography) associated with the marker

• x_seed
• y_seed
• z_seed

--

• is_target: True if the marker is a stimulation target and False otherwise
• session_id: integer containing the number of the session to which the marker belongs

Marker location in the world coordinates

• x_world
• y_world
• z_world

Marker orientation (Euler angles, degrees) in the world coordinates:

• alpha_world
• beta_world
• gamma_world

All the string values are enclosed in quotation marks.

[^1]: Older versions of Invesalius used another file format for storing markers. This legacy format had an extension of .mks and contained only values of the marker attributes (unlike the new format, which also contains some metadata, like version number, attribute names, etc.). Each line in the file corresponded to one marker. The values were stored as text, one line per marker. Within the line the values were separated by tabs. The first three fields of each line were XYZ coordinates, the rest varied. In general, you should not be using the old format. If, for some reason, you have data in the legacy format, you should convert it to the new .mkss format.