atlaslabeler(1) query stereotaxic atlases


atlaslabeler [OPTIONS] [input_file.nii.gz]


show program's version number and exit
-v VERBOSE, --verbose=VERBOSE, --verbosity=VERBOSE
Verbosity level of output
-h, --help, --sos
Show this help message and exit
-a ATLASFILE, --atlas-file=ATLASFILE
Atlas file to use. Overrides --atlas-path and --atlas
Path to the atlas files. '%(name)s' will be replaced with the atlas name. See -A. Defaults depend on the atlas family.
Atlas to use. Choices: HarvardOxford-Subcortical, Juelich, JHU-tracts, HarvardOxford-Cortical, MNI, talairach, Thalamus, talairach-dist
-i INPUTCOORDFILE, --input-coordinates-file=INPUTCOORDFILE
Fetch coordinates from ASCII file
Output file. Otherwise standard output
When working with reference/distance atlases, what maximal distance to use to look for the voxel of interest
First transformation to apply to the data. Usually should be subject -> standard(MNI) transformation
-s, --summary
Either to create a summary instead of dumping voxels. Use multiple -s for greater verbose summary
How to sort summary entries. a-p sorts anteriorposterior order
If original data is given as image file, dump indexes per each treholded voxels into provided here output file
-l LEVELS, --levels=LEVELS
Indexes of levels which to print, or based on which to create a summary (for a summary levels=4 is default). To get listing of known for the atlas levels, use '-l list'
Choose between available transformations from mni 2 talairach space
Lower threshold for voxels to output
Upper threshold for voxels to output
--abbr, --abbreviated-labels
Manipulate with abbreviations for labels instead of full names, if the atlas has such
-c, --tc, --show-target-coord
Show target coordinates
--tv, --show-target-voxel
Show target coordinates
--rc, --show-referenced-coord
Show referenced coordinates/distance in case if we are working with reference atlas
-C, --oc, --show-orig-coord
Show original coordinates
-V, --show-values
Show values
Space in which input volume/coordinates provided in. For instance Talairach/MNI
-F, --forbid-direct-mapping
If volume is provided it first tries to do direct mapping voxel-2-voxel if there is no transformation file given. This option forbids such behavior and does coordinates mapping anyway.
-t, --talairach
Coordinates are in talairach space (1x1x1mm), otherwise assumes in mni space (2x2x2mm). Shortcut for '-I Talairach'
-H, --half-voxel-correction
Adjust coord by 0.5mm after transformation to Tal space. Please use -H to turn such adjustment off
-r, --relative-to-origin
Coords are relative to the origin standard form ie in spatial units (mm), otherwise the default assumes raw voxel dimensions
Format of the input lines (if ASCII input is provided)
Which level to reference in the case of reference atlas
At what probability (in %) to threshold in probabilistic atlases (e.g. FSL)
What strategy to use for reporting. 'max' would report single area (above threshold) with maximal probabilitity


bin/atlaslabeler -s -A talairach-dist -d 10 -R Closest\ Gray -l Structure,Brodmann\ area -cC mask.nii.gz

produces a summary per each structure and brodmann area, for each voxel looking within 10mm radius for the closest gray matter voxel.