brains:BRAINSTalairachMask

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Summary

This program creates a binary image representing the specified Talairach region. The input is an example image to define the physical space for the resulting image, the Talairach grid representation in VTK format, and the file containing the Talairach box definitions to be generated. These can be combined in BRAINS to create a label map using the procedure Brains::WorkupUtils::CreateLabelMapFromBinaryImages.

Authors

• Vincent A. Magnotta
• Steve Dunn

Usage

  BRAINSTalairachMask  [--returnparameterfile <std::string>]
                       [--processinformationaddress
                       <std::string>] [--xml] [--echo]
                       [--outputVolume <std::string>] [--expand]
                       [--hemisphereMode <left|right|both>]
                       [--talairachBox <std::string>]
                       [--talairachParameters <std::string>]
                       [--inputVolume <std::string>] [--]
                       [--version] [-h]

Where:

--returnparameterfile <std::string>
Filename 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)

--outputVolume <std::string>
Output filename for the resulting binary image

--expand
Expand exterior box to include surface CSF (default: 0)

--hemisphereMode <left|right|both>
Mode for box creation: left, right, both (default: both)

--talairachBox <std::string>
Name of the Talairach box file.

--talairachParameters <std::string>
Name of the Talairach parameter file.

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

--, --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

Talairach box based regions showing frontal, temporal, parietal and occipital regions.

Talairach Box File Format

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.