ATLASLABELER(1) 						   User Commands						   ATLASLABELER(1)

NAME

       atlaslabeler - query stereotaxic atlases

SYNOPSIS

       atlaslabeler [OPTIONS] [input_file.nii.gz]

OPTIONS

       --version
	      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

       --atlas-path=ATLASPATH
	      Path to the atlas files. '%(name)s' will be replaced with the atlas name. See -A. Defaults depend on the atlas family.

       -A ATLASNAME, --atlas=ATLASNAME
	      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

       -o OUTPUTFILE, --output-file=OUTPUTFILE
	      Output file. Otherwise standard output

       -d MAXDISTANCE, --max-distance=MAXDISTANCE
	      When working with reference/distance atlases, what maximal distance to use to look for the voxel of interest

       -T TRANSFORMATIONFILE, --transformation-file=TRANSFORMATIONFILE
	      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

       --ss=SORTSUMMARYBY, --sort-summary-by=SORTSUMMARYBY
	      How to sort summary entries.  a-p sorts anteriorposterior order

       --dumpmap-file=DUMPMAPFILE
	      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'

       --mni2tal=MNI2TALTRANSFORMATION
	      Choose between available transformations from mni 2 talairach space

       --thr=LOWERTHRESHOLD, --lthr=LOWERTHRESHOLD, --lower-threshold=LOWERTHRESHOLD
	      Lower threshold for voxels to output

       --uthr=UPPERTHRESHOLD, --upper-threshold=UPPERTHRESHOLD
	      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

       -I INPUTSPACE, --input-space=INPUTSPACE
	      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 for-
	      bids 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

       --input-line-format=INPUTLINEFORMAT
	      Format of the input lines (if ASCII input is provided)

       -R REFERENCELEVEL, --reference=REFERENCELEVEL
	      Which level to reference in the case of reference atlas

       --prob-thr=PROBTHR
	      At what probability (in %) to threshold in probabilistic atlases (e.g. FSL)

       --prob-strategy=PROBSTRATEGY
	      What strategy to use for reporting. 'max' would report single area (above threshold) with maximal probabilitity

EXAMPLES

       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.

atlaslabeler 0.4.8						    April 2012							   ATLASLABELER(1)