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       atlaslabeler - 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.

       -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

              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

              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

       --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

       -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

              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.