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.

pymvpa2-atlaslabeler 2.2.0                        February 2014                          PYMVPA2-ATLASLABELER(1)