,
brings up the landmark window:Landmarks are 3D coordinates (voxel locations) that can be used for positional normalization, cropping and for warping one scan onto another. The origin for these coordinates values is the right-superior-posterior corner of the original (uncropped) scan (see scan coordinate system).
Clicking on the Landmark Tool, ,
brings up the landmark window:
This window lets you see and adjust the locations of existing landmarks and to create new landmarks. The "File" menu allows saving and loading of all landmarks in a file and the "Landmark" menu allows the creation of new individual landmarks.
Clicking below "Choose a Landmark" will pop up a menu of existing landmarks. When one is chosen, each view will be adjusted to show (jump to) that landmark. Above, "AC_POINT" (the anterior commisure) is chosen. When using the landmark tool, clicking the left mouse button in an image will move the currently chosen landmark to that mouse click location in 3D. The text display shows the exact (uncropped) position of that landmark and the arrow buttons allow the landmark to be nudged around. The nudge size is controlled by the number ("0.5" above) inside the arrows. The "Next" and "Previous" buttons step through each landmark by making all images show that landmark. This is the coronal image after selecting the AC_POINT:
Note that the red projection lines go through the landmark. This means that the other two views are also showing that landmark.
Landmarks are associated with each individual scan. Note above, where it says"Choose a scan", the choice is set to "11_10". Leave this at the default setting which is the MRI brain image scan. It is possible to set this choice to modify landmarks for the Contour and Outline scans, but this is reserved for future features.
When NVM starts up, it reads a default landmark file, usually in:
$NVM_HOME/Landmark/defaultLandmark.xml
The purpose of this landmark file is to define the usual landmarks: AC_POINT, PC_POINT, MID_SAGITTAL_POINT, MAX_CROP, and MIN_CROP and give them an "undefined" value of "-1".
The default landmark file can be changed in the preferences under the "Tools: Landmark" tabs. See "Initial landmark file to laod when starting".
The standard place and name for a landmark file is:
<Path to result files>/<pid>/<scn>/otl/<segmenter prefix>_Landmark.xml
e.g.: /Data/11/10/ajw_Landmark.xml
This is used when saving and loading landmarks using the File menu in the Landmark tool window (shown above).
The location of the landmark file can be set to an arbitrary path in the preferences under the "Tools: Landmark" tabs. In this case, the file name will be "Landmark.xml" (without the <segmenter prefix> attached).
NVM reads the default landmark file first to define the names of the standard landmarks, but no cropping information is in this file. NVM gets cropping information from the info file if it is present. But before actually loading the scan data, NVM also reads the standard landmark file. This way the standard landmark file overrides the info file landmarks.