= Command-line reconstruction interface = Apart from GUI, the 3D Brain Atlas Reconstructor comes with command line interface (or shorter: CLI) allowing the user to perform batch reconstructions without configured graphics environment. After invoking the batch interface, following information will appear: {{{ $./batchinterface.sh Usage: ./batchinterface.sh [options] [ [ ...]] 3d Brain Atlas Reconstructor ver.ver. 0.1 Batch reconstruction interface Options: --version show program's version number and exit -h, --help show this help message and exit -g GENERATESUBSTRUCTURES, --generateSubstructures=GENERATESUBSTRUCTURES maximum level of substructures (in the structure tree) to be generated; defaults to 0 -d VOXELDIMENSIONS, --voxelDimensions=VOXELDIMENSIONS voxel size [mm] (in coronal plane, along anterior- posterior axis) -e EXPORTDIR, --exportDir=EXPORTDIR the path to a directory for reconstructions -p PIPELINE, --usePipeline=PIPELINE the path to a custom pipeline definition -a CAMERAMOVEMENTANGLES, --cameraMovementAngles=CAMERAMOVEMENTANGLES camera movement angles (azimuth, elevation, roll) -b BACKGROUND, --background=BACKGROUND RGB background colourcomponents (within 0.0-255.0 range) --exportToWindow, --show the reconstruction is displayed to the user --composite perform a reconstruction of the structure as a scene composed of the reconstructions of the basic substructures in the hierarchy tree (up to the maximum given level) --includeBrainOutline Includes additional translucent brain outline to the reconstructions. Applies only when exporting to VRML, X3D or thumbnail. --ignoreBoundingBox Overrides bounding box calculation - bounding box will be always equal to hierarchy root element bounding box. Volumes for all structures will always have the same size and origin. This feature increases memory usage and reconstruction time. Output Format Options: --exportToX3d exports as X3D scene --exportToVRML exports as VRML scene --exportToPOVRay exports to POV-Ray --exportToVTKPolydata exports as VTKpolyMesh --exportToVolume exports as VTKstructGrid --exportToNiftii exports as Niftii file --exportToNumpy exports as Numpy array --exportScreenshot saves screenshot as an PNG image --exportThumbnail saves scaled screenshot as an PNG image }}} The `` is a location of the index file of the given CAF dataset while the `[ [ ...]]` is space-separated list of all structures to reconstruction contained in the CAF dataset. The simplest usage of the CLI is to generate reconstruction of a single structure from provided CAF dataset using default settings. Assume that our CAF dataset is located in the `~/atlases/mouse/caf/` directory and we would like to reconstruct the ''Thalamus'' and save a nifti volume with the reconstruction: {{{ $./batchinterface.sh ~/atlases/mouse/caf/index.xml Thalamus --exportToNiftii }}} By default, the reconstructions of requested structures generated with predefined voxel dimensions, pipeline and camera position and stored in directory parallel to the CAF dataset directory (in this example it would be `~/atlases/mouse/reconstructions/`). However, this behavior can be customized with commandline options.