.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.9.
.TH ATLASLABELER "1" "April 2012" "atlaslabeler 0.4.8" "User Commands"
.SH NAME
atlaslabeler \- query stereotaxic atlases
.SH SYNOPSIS
.B atlaslabeler
[\fIOPTIONS\fR] [\fIinput_file.nii.gz\fR]
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-v\fR VERBOSE, \fB\-\-verbose\fR=\fIVERBOSE\fR, \fB\-\-verbosity\fR=\fIVERBOSE\fR
Verbosity level of output
.TP
\fB\-h\fR, \fB\-\-help\fR, \fB\-\-sos\fR
Show this help message and exit
.TP
\fB\-a\fR ATLASFILE, \fB\-\-atlas\-file\fR=\fIATLASFILE\fR
Atlas file to use. Overrides \fB\-\-atlas\-path\fR and \fB\-\-atlas\fR
.TP
\fB\-\-atlas\-path\fR=\fIATLASPATH\fR
Path to the atlas files. '%(name)s' will be replaced
with the atlas name. See \fB\-A\fR. Defaults depend on the
atlas family.
.TP
\fB\-A\fR ATLASNAME, \fB\-\-atlas\fR=\fIATLASNAME\fR
Atlas to use. Choices: HarvardOxford\-Subcortical,
Juelich, JHU\-tracts, HarvardOxford\-Cortical, MNI,
talairach, Thalamus, talairach\-dist
.TP
\fB\-i\fR INPUTCOORDFILE, \fB\-\-input\-coordinates\-file\fR=\fIINPUTCOORDFILE\fR
Fetch coordinates from ASCII file
.TP
\fB\-o\fR OUTPUTFILE, \fB\-\-output\-file\fR=\fIOUTPUTFILE\fR
Output file. Otherwise standard output
.TP
\fB\-d\fR MAXDISTANCE, \fB\-\-max\-distance\fR=\fIMAXDISTANCE\fR
When working with reference/distance atlases, what
maximal distance to use to look for the voxel of
interest
.TP
\fB\-T\fR TRANSFORMATIONFILE, \fB\-\-transformation\-file\fR=\fITRANSFORMATIONFILE\fR
First transformation to apply to the data. Usually
should be subject \-> standard(MNI) transformation
.TP
\fB\-s\fR, \fB\-\-summary\fR
Either to create a summary instead of dumping voxels.
Use multiple \fB\-s\fR for greater verbose summary
.TP
\fB\-\-ss\fR=\fISORTSUMMARYBY\fR, \fB\-\-sort\-summary\-by\fR=\fISORTSUMMARYBY\fR
How to sort summary entries.  a\-p sorts anteriorposterior order
.TP
\fB\-\-dumpmap\-file\fR=\fIDUMPMAPFILE\fR
If original data is given as image file, dump indexes
per each treholded voxels into provided here output
file
.TP
\fB\-l\fR LEVELS, \fB\-\-levels\fR=\fILEVELS\fR
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'
.TP
\fB\-\-mni2tal\fR=\fIMNI2TALTRANSFORMATION\fR
Choose between available transformations from mni 2
talairach space
.TP
\fB\-\-thr\fR=\fILOWERTHRESHOLD\fR, \fB\-\-lthr\fR=\fILOWERTHRESHOLD\fR, \fB\-\-lower\-threshold\fR=\fILOWERTHRESHOLD\fR
Lower threshold for voxels to output
.TP
\fB\-\-uthr\fR=\fIUPPERTHRESHOLD\fR, \fB\-\-upper\-threshold\fR=\fIUPPERTHRESHOLD\fR
Upper threshold for voxels to output
.TP
\fB\-\-abbr\fR, \fB\-\-abbreviated\-labels\fR
Manipulate with abbreviations for labels instead of
full names, if the atlas has such
.TP
\fB\-c\fR, \fB\-\-tc\fR, \fB\-\-show\-target\-coord\fR
Show target coordinates
.TP
\fB\-\-tv\fR, \fB\-\-show\-target\-voxel\fR
Show target coordinates
.TP
\fB\-\-rc\fR, \fB\-\-show\-referenced\-coord\fR
Show referenced coordinates/distance in case if we are
working with reference atlas
.TP
\fB\-C\fR, \fB\-\-oc\fR, \fB\-\-show\-orig\-coord\fR
Show original coordinates
.TP
\fB\-V\fR, \fB\-\-show\-values\fR
Show values
.TP
\fB\-I\fR INPUTSPACE, \fB\-\-input\-space\fR=\fIINPUTSPACE\fR
Space in which input volume/coordinates provided in.
For instance Talairach/MNI
.TP
\fB\-F\fR, \fB\-\-forbid\-direct\-mapping\fR
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.
.TP
\fB\-t\fR, \fB\-\-talairach\fR
Coordinates are in talairach space (1x1x1mm),
otherwise assumes in mni space (2x2x2mm). Shortcut for
\&'\-I Talairach'
.TP
\fB\-H\fR, \fB\-\-half\-voxel\-correction\fR
Adjust coord by 0.5mm after transformation to Tal
space. Please use \fB\-H\fR to turn such adjustment off
.TP
\fB\-r\fR, \fB\-\-relative\-to\-origin\fR
Coords are relative to the origin standard form ie in
spatial units (mm), otherwise the default assumes raw
voxel dimensions
.TP
\fB\-\-input\-line\-format\fR=\fIINPUTLINEFORMAT\fR
Format of the input lines (if ASCII input is provided)
.TP
\fB\-R\fR REFERENCELEVEL, \fB\-\-reference\fR=\fIREFERENCELEVEL\fR
Which level to reference in the case of reference
atlas
.TP
\fB\-\-prob\-thr\fR=\fIPROBTHR\fR
At what probability (in %) to threshold in
probabilistic atlases (e.g. FSL)
.TP
\fB\-\-prob\-strategy\fR=\fIPROBSTRATEGY\fR
What strategy to use for reporting. 'max' would report
single area (above threshold) with maximal
probabilitity
.SH EXAMPLES

bin/atlaslabeler \fB\-s\fR \fB\-A\fR talairach\-dist \fB\-d\fR 10 \fB\-R\fR Closest\e Gray \fB\-l\fR Structure,Brodmann\e area  \fB\-cC\fR mask.nii.gz
.PP
produces a summary per each structure and brodmann area, for each voxel
looking within 10mm radius for the closest gray matter voxel.