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.