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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.