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ATLAS 3.8.1 (Default branch)
02-28-2008
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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)