NAME

       pymvpa2-atlaslabeler - query stereotaxic atlases

SYNOPSIS

       pymvpa2-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 [Default: 0]

       -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

       -f ATLASIMAGEFILE, --atlas-image-file=ATLASIMAGEFILE
              Path  to  the  data  image  for  the  corresponding atlas.  Can be used to override
              default image if it was already resliced into a corresponding space (e.g.  subject)

       -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

       --count-thr=COUNTTHRESHOLD, --cthr=COUNTTHRESHOLD
              Lowest number of voxels for area to be reported in summary

       --count-pthr=COUNTPERCENTTHRESHOLD, --pthr=COUNTPERCENTTHRESHOLD
              Lowest percentage of voxels within an area to be reported in summary

       --suppress-none, --sn
              Suppress reporting of voxels which found no labels (reported as None)

       --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.

       -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)

       --iv, --input-voxels
              Input lines carry voxel indices (int), not coordinates.

       -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

       > pymvpa2-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.

       Simpler, more reliable, and faster usage is by  providing  a  corresponding  atlas  volume
       image registered to the volume at hands, e.g.:

       >    pymvpa2-atlaslabeler   -f   MNI-prob-bold.nii.gz   -A   MNI   -s   mask_vt.nii.gz   >
       pymvpa2-atlaslabeler -f HarvardOxford-cort-prob-bold.nii.gz -A  HarvardOxford-Cortical  -s
       mask_vt.nii.gz

       would  provide  summary  over  the MNI (or HarvardOxford-Cortical) atlas, .nii.gz of which
       were previously flirted (or fnirted) into the space of mask_vt.nii.gz and provided in '-f'
       argument.