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.