brains:BRAINSSurfaceGeneration

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Contents 1 Summary 2 Authors 3 Usage 4 Figures 5 References 5.1 Methods 5.2 Applications 6 Acknowledgements

Summary

This program can takes two kinds of inputs, itk images or vtk surfaces.

The surface decimation and smoothing will be applied on the generated surface.

The primary purpose of this program is to generate the cortical surface of the brain.

Authors

• Wen Li
• Vincent Magnotta

Usage

BRAINSSurfaceGeneration  
[--inputImageFile <std::string>] 
[--inputSurfaceFile <std::string>]
[--outputSurface <std::string>]
[--surfaceValue <double>]
[--genusNumber]
[--decimateSurface]
[--numberOfElements <integer>]
[--smoothSurface]
[--numIterations <integer>
[--relaxationFactor <double>]
[--help]

Where:

---inputImageFile <std::string>
Filename of the input itk image

---inputSurfaceFile <std::string>
Filename of the input vtk surface

---outputSurface
Filename of the output surface (.vtk)

---surfaceValue
The iso-value of the input image to generate the surface

If it is a binary image, this value should be 0.5 (default). If it is a gray level image, the value should be 0.5 lower than the actual iso-value you would want the surface to be. For example, if the surface is generated at 130, this value should be set to 129.5.

---genusNumber
Turn on to print the number of genus at the output surface (default: OFF)

---decimateSurface
Turn on to decimate the surface (default: OFF)

---numberOfElements <integer>
The number of elements (triangles) to be left on the output surface if -decimateSurface is ON

---smoothSurface
Turn on surface smoothing (default: OFF)

---numIterations <integer>
The number of iterations for surface smoothing if -smoothSurface is ON (default: 5)

--relaxationFactor <double>
The relaxation factor for surface smoothing and bigger value of it results smoother surface (default: 0.1)

---help
Displays the parameters to run this command

Figures

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.