Reading Data
This section describes how to convert FITS data into NRRD files readable by Slicer, and how to read this data into Slicer. It also describes how pre-created scenes can be viewed.
FITS Conversion
FITS data cannot be directly read into 3D Slicer. Instead, use our fits2itk FITS converter command line tool to create a file that Slicer can handle. At present, all coordinate information is lost during this step. Future versions of Slicer will, however, have an integrated FITS reader and handle celestial coordinate systems.
The example FITS data (24 MB) consists of two maps of the L1448 molecular cloud in Perseus. You may also use pre-created NRRD files (24 MB), in case you prefer to skip the FITS-to-NRRD conversion. One map, L1448_13CO.fits, gives the 13CO (J=1-0) intensity distribution in L1448, as observed by the FCRAO telescope. The intensity information is encoded using real numbers. The other file, L1448_13CO-CLUMPFIND.fits, gives the positions of "clumps" identified in the former map by using the CLUMPFIND algorithm. Whether a voxel belongs to clump number n is encoded using integer numbers. Details on the datasets are given in our description of Perseus scenes.
The FITS data is converted into NRRD files using the commands
fits2itk -A -a1000 -r-1 -s1000 L1448_13CO.fits L1448_13CO.nrrd
and
fits2itk -A -a1000 -r-1 L1448_13CO-CLUMPFIND.fits L1448_13CO-CLUMPFIND.nrrd .
Please refer to the fits2itk documentation for an explanation of the options. Note that the option "-s1000", which scales voxel values up by a factor 1000, is only needed when processing the file L1448_13CO.fits. This dataset contains real numbers, for which only limited support exists within 3D Slicer. The data must be scales to preserve its dynamic range, since real numbers are usually (depending on the Slicer version) converted into integers within 3D Slicer.
In the example case, an intensity value of 3400 in the L1448_13CO.nrrd file corresponds to an intensity of 3.4 K in L1448_13CO.fits. The "-s1000" option effectively converts the intensity scale from Kelvin to milli Kelvin.
Reading NRRD Data into Slicer
You can read NRRD datasets individually into Slicer. Such datacubes are called "volumes" within Slicer. In analogy to the pixels in 2D graphics, the basic elements of volumes are volume elements, or voxels. To read data, first hit the 'Data' button in the main menu, and then 'Add Volume' in the panel below. This takes you to the 'Props' tab in the 'Volumes' panel.
Set 'Active Volume' to 'NEW', and the 'Properties' selector to 'Generic Readers'. You can select a file after hitting the 'Browse...' button, which takes you to a new window. After selecting your file you must specify whether the data is to be read in as 'Greyscale' (e.g., an intensity map) or as a 'Label Map' (e.g., output from clump-finding algorithms). Optionally you might give a name to the dataset in the 'Name:' field. Leave the other selectors set to their default value. Finally, hit 'Apply' to read the data, or select 'Cancel' to abort.
For our excercise, read L1448_13CO.nrrd as a greyscale file named "IntensityMap", and read L1448_13CO-CLUMPFIND.nrrd as a label map named "CLUMPFINDLabels".
Reading Scenes
Data can also be read in pre-created bundles called "scenes". A scene file contains the information which data was viewed using what viewing options. Scenes are, e.g., used in the tour on iso-intensity surfaces in L1448. Please refer to that tour for details.
Now proceed to data navigation.