brains:BRAINSAssignSurfaceFeatures

From NITRC Wiki

Summary

Ths program calculate several types of geometry features (distanceFromPC, depth to a hull, cortical thickness, and mean_curvature) on the input surface. The geometry features will be added as arrays of the vtkPolyData of the output surface. If cortical thickness needs to be calculated, the input surface should be the inner surface.

Authors

• Wen Li
• Vincent Magnotta

Usage

BRAINSAssignSurfaceFeatures  
[--inputSurfaceFile <std::string>] 
[--outerSurfaceFile <std::string>]
[--outputSurfaceFile <std::string>]
[--distanceToPC_AP]
[--distanceToPC_IS]
[--PC <double-vector>]
[--distanceToHull]
[--corticalThickness]
[--maxThickness <double>]
[--curvature]
[--curvatureType <string-enumeration>]
[--help]

Where:

---inputSurfaceFile <std::string>
File name of the input surface (.vtk)

---outerSurfaceFile <std::string>
File name of the outer vtk surface (.vtk) when corticalThickness is ON

---outputSurfaceFile <std::string>
Filename of the output surface (.vtk)

---distanceToPC_AP
Turn on to calculate the geometry feature of distanceToPC in the direction of Anterior-to-Posterior (default: OFF)

---distanceToPC_IS
Turn on to calculate the geometry feature of distanceToPC in the direction of Inferior-to-Superior (default: OFF)

---PC <double-vector>
Location of PC Point (x y z)

---distanceToHull
Turn on to calculate the geometry feature of distance to a convex hull of the input surface (default: OFF)

---corticalThickness
Turn on to calculate the geometry feature of cortical thickness (default: OFF)

---maxThickness <double>
The expected maximum cortical thickness (unit: mm). The resulting cortical thickness is set to be this value if the  calculated value is bigger than it (default: 7.5)

--curvature
Turn on to calculate the geometry feature of curvature (default: OFF)

--curvatureType  <string-enumeration>
The type of curvature to be calculated (Mean|Gauss default: Mean)

--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.