brains:BRAINSMeasureSurface

From NITRC Wiki

Return to brains:mainPage

Summary

This program generates measures regional statistics of a surface based on the scalars associated with the triangles. Regional measures for surface area, cortical thickness, and curvature are written to either a CSV or XML file. You must have a labeled VTK surface to work with this program. The user specifies the label name to be used in the measurements. It is assumed that the surface also contains the following data arrays

• Mean_Curvature - Curvature measures
• Depth - Depth measurements

In the future the names of these arrays will be added to the command line for flexibility. Currently only the CSV output is supported. We are currently working to add the XML format.

Authors

• Vincent Magnotta

Usage

BRAINSMeasureSurface  [--returnparameterfile <std::string>]
                      [--processinformationaddress <std::string>] 
                      [--xml] [--echo]
                      [--sulcalCurvatureResults <std::vector<double>>]
                      [--gyralCurvatureResults <std::vector<double>>]
                      [--totalCurvatureResults <std::vector<double>>]
                      [--testCurvature]
                      [--sulcalAreaResults <std::vector<double>>]
                      [--gyralAreaResults <std::vector<double>>]
                      [--totalAreaResults <std::vector<double>>] 
                      [--testArea]
                      [--sulcalDepthResults <std::vector<double>>]
                      [--gyralDepthResults <std::vector<double>>]
                      [--totalDepthResults <std::vector<double>>]
                      [--testDepth] 
                      [--xmlFile <std::string>] 
                      [--csvFile <std::string>] 
                      [--writeXmlFile]
                      [--writeCsvFile] 
                      [--scanId <std::string>] 
                      [--subjectId <std::string>] 
                      [--labelNames <std::vector<std::string>>]
                      [--arrayName <std::string>]
                      [--inputSurface <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)

--sulcalCurvatureResults <std::vector<double>>
Expected sulcal curvature for each label (default: None)

--gyralCurvatureResults <std::vector<double>>
Expected gyral curvature for each label (default: None)

--totalCurvatureResults <std::vector<double>>
Expected total curvature for each label (default: None)

--testCurvature
Test curvature measurements (default: 0)

--sulcalAreaResults <std::vector<double>>
Expected sulcal surface area for each label (default: None)

--gyralAreaResults <std::vector<double>>
Expected gyral surface area for each label (default: None)

--totalAreaResults <std::vector<double>>
Expected total surface area for each label (default: None)

--testArea
Test surface area measurements (default: 0)

--sulcalDepthResults <std::vector<double>>
Expected sulcal depth measurements for each label (default: None)

--gyralDepthResults <std::vector<double>>
Expected gyral depth measurements for each label (default: None)

--totalDepthResults <std::vector<double>>
Expected total depth measurements for each label (default: None)

--testDepth
Test Cortical depth measurements (default: 0)

--xmlFile <std::string>
Output XML Result filename

--csvFile <std::string>
Output CSV Rsult filename

--writeXmlFile
Boolean Flag to specify if a XML file is to be written (default: 0)

--writeCsvFile
Boolean Flag to specify if a CSV file is to be written (default: 0)

--scanId <std::string>
Scan ID to be used for labeling of results

--subjectId <std::string>
Subject ID to be used for labeling of results

--labelNames <std::vector<std::string>>
Names for the anatomical labels (default: None)

--arrayName <std::string>
Array name containing the anatomical labels (default: None)

--inputSurface <std::string>
Input Surface Filename

--, --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

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.