brains:BRAINSSurfaceRegistration

From NITRC Wiki

Summary

This program does multiresolution registration on two lists of spheres associated with scalar values.

Authors

• Wen Li
• Luis Ibanez
• Vincent Magnotta

Usage

BRAINSSurfaceRegistration 
[--fixedMeshFileList]
[--movingMeshFileList]
[--fixedMeshFileName]
[--movingMeshFileName]
[--rigidIterations <integer-vector>]
[--demonsIterations <integer-vector>]
[--smoothIterations <integer-vector>]
[--metricSignificance <double-vector>]
[--resolutionLevels <integer>] 
[--deformedFileNameRes4]
[--deformedFileName]
[--deformationFieldFileName]
[--help]

Where:

---fixedMeshFileList
The list of filenames (.vtk) of the fixed meshes with one file at one resolution to be the fixed sphere at that level. The filenames are separated by comma.

---movingMeshFileList
The list of filenames (.vtk) of the moving meshes with one file at one resolution to be the moving sphere at that level. The filenames are separated by comma.

---fixedMeshFileName
The filename of the original fixed mesh, either with or without scalar values is fine (.vtk)

---movingMeshFileName
The filename of the original moving mesh, either with or without scalar values is fine (.vtk)

---rigidIterations <integer-vector>
The number of iterations to run rigid (rotational) registration at each resolution level

---demonsIterations <integer-vector>
The number of iterations to run nonrigid (spherical demons) registration at each resolution level

---smoothIterations <integer-vector>
The number of iterations to smooth the deformation field at each resolution level

---metricSignificance <double-vector>
The demons registration stops when the change of metric (in percentage of the metric value of the last iteration) is smaller than the specified value here at the corresponding resolution level

---resolutionLevels <integer>
The number of resolution levels to do the registration (required to be 4)

---deformedFileNameRes4
The filename of deformed fixed sphere at level 4 -- the highest resolution level

---deformedFileName
The filename of deformed original fixed sphere

---deformationFieldFileName
The filename of the deformation field as vectors associated with the input original fixed sphere. It keeps the displacement between the input original fixed sphere and the deformed original fixed sphere

--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.