brains:BRAINSApplySurfaceLabels

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Summary

This program takes in a label map and a surface and labels the surface. The images as defined in ITK is in an LPS coordinate system while the surface is expected to be in an RAS coordinate system to support integration with the 3D Slicer program. Currently the cells (i.e. triangles) of the surface based on a voting rule. If all three points have a different labels then the cell is arbitrarily assigned to one of the labels.

Authors

• Steve Dunn
• Vincent Magnotta

Usage

BRAINSApplySurfaceLabels  [--returnparameterfile <std::string>]
                          [--processinformationaddress <std::string>] 
                          [--xml] [--echo]
                          [--outputSurface <std::string>]
                          [--cellDataName <std::string>]
                          [--inputSurface <std::string>]
                          [--inputLabelMap <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)

--outputSurface <std::string>
Output Surface

--cellDataName <std::string>
Cell Data Name

--inputSurface <std::string>
Input Surface

--inputLabelMap <std::string>
Input Label Map

--, --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 surface Labels

References

Methods

1. Magnotta VA, Andreasen NC, Schultz SK, Harris G, Cizadlo T, Heckel D, Nopoulos P, Flaum M. Quantitative in vivo measurement of gyrification in the human brain: changes associated with aging. Cereb Cortex. 1999 Mar;9(2):151-60.
2. Magnotta VA, Harris G, Andreasen NC, O'Leary DS, Yuh WT, Heckel D. Structural MR image processing using the BRAINS2 toolbox. Comput Med Imaging Graph. 2002 Jul-Aug;26(4):251-64.

Applications

1. Crespo-Facorro B, Kim JJ, Andreasen NC, O'Leary DS, Wiser AK, Bailey JM, Harris G, Magnotta VA. Human frontal cortex: an MRI-based parcellation method. Neuroimage. 1999 Nov;10(5):500-19.
2. Crespo-Facorro B, Kim J, Andreasen NC, O'Leary DS, Magnotta V. Regional frontal abnormalities in schizophrenia: a quantitative gray matter volume and cortical surface size study. Biol Psychiatry. 2000 Jul 15;48(2):110-9.
3. Crespo-Facorro B, Kim J, Andreasen NC, O'Leary DS, Bockholt HJ, Magnotta V. Insular cortex abnormalities in schizophrenia: a structural magnetic resonance imaging study of first-episode patients. Schizophr Res. 2000 Nov 30;46(1):35-43. Erratum in: Schizophr Res 2001 Sep 1;51(2-3):183-4.
4. Chemerinski E, Nopoulos PC, Crespo-Facorro B, Andreasen NC, Magnotta V. Morphology of the ventral frontal cortex in schizophrenia: relationship with social dysfunction. Biol Psychiatry. 2002 Jul 1;52(1):1-8.
5. White T, Andreasen NC, Nopoulos P, Magnotta V. Gyrification abnormalities in childhood- and adolescent-onset schizophrenia. Biol Psychiatry. 2003 Aug 15;54(4):418-26.
6. Oyegbile T, Hansen R, Magnotta V, O'leary D, Bell B, Seidenberg M, Hermann BP. Quantitative measurement of cortical surface features in localization-related temporal lobe epilepsy. Neuropsychology. 2004 Oct;18(4):729-37.
7. Crespo-Facorro B, Nopoulos PC, Chemerinski E, Kim JJ, Andreasen NC, Magnotta V. Temporal pole morphology and psychopathology in males with schizophrenia. Psychiatry Res. 2004 Dec 15;132(2):107-15.

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.