brains:BRAINSTalairach

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Summary

This program creates a VTK structured box/grid defining the Talairach coordinate system based on four points:

1. AC
2. PC
3. IRP
4. SLA

Two representations of the resulting grid can be written. The first is a bounding box representation that also contains the location of the AC and PC points. The second representation is the full Talairach grid representation that includes the additional rows of boxes added to the inferior allowing full coverage of the cerebellum.

Authors

• Vincent A. Magnotta
• Steve Dunn

Usage

  BRAINSTalairach  [--returnparameterfile <std::string>]
                   [--processinformationaddress <std::string>]
                   [--xml] [--echo] [--outputGrid <std::string>]
                   [--outputBox <std::string>] [--inputVolume
                    <std::string>] [--IRPisIndex] [--IRP
                    <std::vector<double>>] [--SLAisIndex] [--SLA
                    <std::vector<double>>] [--PCisIndex] [--PC
                    <std::vector<double>>] [--ACisIndex] [--AC
                    <std::vector<double>>] [--] [--version] [-h]

--returnparameterfile <std::string>
File name in which to write simple return parameters (int, float, int-vector, etc.) as opposed to bulk return parameters (image,geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort, etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--outputGrid <std::string>
Name of the resulting Talairach Grid file. If the file extension is .vtk then the file is written in the old VTK format otherwise the new VTK XML file format is used.

--outputBox <std::string>
Name of the resulting Talairach Bounding Box file. If the file extension is .vtk then the file is written in the old VTK format otherwise the new VTK XML file format is used.

--inputVolume <std::string>
Input image used to define physical space of images

--IRPisIndex
IRP Point is Index (default: 0)

--IRP <std::vector<double>>
Location of IRP Point

--SLAisIndex
SLA Point is Index (default: 0)

--SLA <std::vector<double>>
Location of SLA Point

--PCisIndex
PC Point is Index (default: 0)

--PC <std::vector<double>>
Location of PC Point

--ACisIndex
AC Point is Index (default: 0)

--AC <std::vector<double>>
Location of AC Point

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

Figures

Bounding Box Talairach Representation

Talairach Grid Representation

References

1. Andreasen NC, Rajarethinam R, Cizadlo T, Arndt S, Swayze VW 2nd, Flashman LA, O'Leary DS, Ehrhardt JC, Yuh WT. Automatic atlas-based volume estimation of human brain regions from MR images. J Comput Assist Tomogr. 1996 Jan-Feb;20(1):98-106.

Acknowledgements

This work was developed by the University of Iowa Departments of Radiology and Psychiatry. This software was supported in part of NIH/NINDS award NS050568.