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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,

       -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

       --thr=LOWERTHRESHOLD,                            --lthr=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

       -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.