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 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

       --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.