brains:BRAINSMarchingCubes

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Summary

This program generates surfaces from itk images with an iso-contour value An anti-aliasing filter is also used to smooth the resulting surface. The primary purpose of this program is to generate the cortical surface of the brain. Measurements for the curvature and cortical thickness can be generated.

Authors

• Wen Li
• Vincent Magnotta

Usage

BRAINSMarchingCubes  [--returnparameterfile <std::string>]
                     [--processinformationaddress <std::string>] 
                     [--xml] [--echo]
                     [--antiAlias]
                     [--normalizeCoordinates]
                     [--featureEdgeSmoothing]
                     [--boundarySmoothing] 
                     [--passBand <double>] 
                     [--numIterations <int>]
                     [--preserveTopology]
                     [--targetReduction <double>]
                     [--writeBinaryFile]
                     [--largestConnected] 
                     [--maxDepth <double>] 
                     [--measureDepth]
                     [--measureCurvature] 
                     [--maxRMSError <double>] 
                     [--contourValue <double>]
                     [--maxSurfaceValue <double>]
                     [--depthSurfaceValue <double>]
                     [--surfaceValue <double>]
                     [--binaryFileName <std::string>]
                     [--outputSurface <std::string>]
                     [--inputFile <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)

--antiAlias
Turn anti-aliasing on or off (default: 0)

--normalizeCoordinates
Turn on Normalize Coordinates Smoothing (default: 0)

--featureEdgeSmoothing
Turn off Feature Edge Smoothing (default: 0)

--boundarySmoothing
Flag to apply smoothing on boundaries (default: 0)

--passBand <double>
The PassBand in Smoothing (default: 0.1)

--numIterations <int>
Number of Iterations Used in Smoothing (default: 50)

--preserveTopology
Topology should be preserved during surface decimation (default: 0)

--targetReduction <double>
Target Reduction for the decimation (default: 0.9999)

--writeBinaryFile
Write a binary image that is topologically correct for surface generation (default: 0)

--largestConnected
Keep only the largest connected region of the surface. (default: 0)

--maxDepth <double>
Limit on maximum depth calculated (default: 4)

--measureDepth
Calculate Cortical Depth (default: 0)

--measureCurvature
Measure Surface Curvature (default: 0)

--maxRMSError <double>
The maximum RMS error for the Anti-Alias filter (default: 0.005)

--contourValue <double>
Contour in binary images to generate the surface (default: 0.5)

--maxSurfaceValue <double>
Maximum value used for create a binary representation (default: 255)

--depthSurfaceValue <double>
The iso-surface value used to measure depth. (default: 190)

--surfaceValue <double>
The iso-surface value for the resulting surface. (default: 130)

--binaryFileName <std::string>
Output binary image filename

--outputSurface <std::string>
Output surface filename

--inputFile <std::string>
Input File Name

--, --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

Brain surface shown in BRAINSTracer

Surface with overlaid surface depth

Surface with overlaid curvature

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.