---
name: "atlaslabeler"
section: "1"
platform: "linux"
package: "python-mvpa"
version: "0.4.8-1"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/atlaslabeler"
---

# atlaslabeler(1)

query stereotaxic atlases

## 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.