Classes
class	BrainIntensities
	Robust statistics for minimum and maximum tissue intensities. More...

Functions
template<class D >
size_t	HeadTopSlice (const Image< D > &img, const std::string &orientation)
	It searches for the first superior axial slice with a pixel which intensity is higher than otsu threshold. More...

template<class D >
Vector< size_t >	COGbyIntensityThreshold (const Image< D > &img)
	Returns a Vector with COG coordinates, based on a binary mask of the image main object. More...

template<class D >
Vector< size_t >	COGbyWeightedIntensity (const Image< D > &img)
	Returns a Vector with COG coordinates, based on intensity weighted values of the image. More...

template<class D >
Vector< size_t >	COGbyHeadTopDistance (const Image< D > &img, const std::string &orientation)
	Returns a Vector with COG coordinates, based on intensity weighted values of the image and distance from the top of the head. More...

template<class D >
Vector< size_t >	COGbyIntegralImage (const Image< D > &img, const std::string &orientation, MRIModality modality)
	Returns a Vector with COG coordinates, based on intensity weighted values of the image and distance from the top of the head. More...

template<class D >
Image< D >	RemoveIntensityOutliers (const Image< D > &img, const Image< D > &msk, float compression, MRIModality modality)
	Remove outliers from brain mask which have extreme intensity values. Used to correct inhomogeneity. More...

template<class D >
Image< D >	BiasSurfaceEstimation (const Image< D > &img, const Image< D > &msk, const Image< D > &cln_msk, float radius, MRIModality modality)
	Computes bias surface based on white matter pixels in the image. More...

template<class D >
Image< D >	BiasSurfaceRemoval (const Image< D > &img, const Image< D > &msk, const Image< D > &bias, MRIModality modality)
	Removes estimated bias field from the input image. More...

template<class D >
Image< D >	InhomogeneityCorrection (const Image< D > &img, const Image< D > &msk, float radius=15.5, size_t compression=2, MRIModality modality=MRIModality::T1)
	Computes bias surface based on white matter pixels in the image. More...

template<class D >
Vector< size_t >	Location (const Image< D > &img, const std::string &orientation, Vector< Box > &best_rectangles, Image< float > &similarity)
	Finds the best location of a box inside the brain and of surrounding boxes outside of the brain. More...

template<class D >
Image< D >	SkullStripping (const Image< D > &img, const std::string &orientation)
	Segments the brain from the background. More...

template<class D >
void	TissueLabeling (const Image< D > &image, const Image< D > &mask, Image< int > &label, D intensity)
	Set labeled clusters into low and high intensity tissues. Low intensity tissue pixels have their label set to 0 and high intensity tissue pixels have their label set to 1. More...

template<class D >
Image< int >	TissueSegmentation (const Image< D > &img, const Image< D > &msk, D tissue_intensity, float scl_min, float scl_max, bool hierarchical)
	Set labeled clusters into low and high intensity tissues. Low intensity tissue pixels have their label set to 0 and high intensity tissue pixels have their label set to 1. More...

template<class D >
Image< int >	TissueSegmentation (const Image< D > &img, const Image< D > &msk, MRIModality modality, float csf_scl_min=0.1, float csf_scl_max=0.2, float gm_scl_min=0.2, float gm_scl_max=0.3, bool hierarchical=false)
	Segment brain into CSF, GM, and WM tissues. More...

Function Documentation

template<class D >

Image< D > Bial::Brain::BiasSurfaceEstimation	(	const Image< D > &	img,
		const Image< D > &	msk,
		const Image< D > &	cln_msk,
		float	radius,
		MRIModality	modality
	)

Computes bias surface based on white matter pixels in the image.

Date: 2014/Jan/08

Parameters

img	A MRI image.
msk	Brain mask.
cln_msk	Brain mask without outliers.
radius	Radius for distance transform. (8.0 to 20.0)
modality	Image modality.

Returns: Image with bias field surface.

Warning: none.

template<class D >

Image< D > Bial::Brain::BiasSurfaceRemoval	(	const Image< D > &	img,
		const Image< D > &	msk,
		const Image< D > &	bias,
		MRIModality	modality
	)

Removes estimated bias field from the input image.

Date: 2014/Jan/08

Parameters

img	A MRI image.
msk	Brain mask.
bias	Bias field surface.
modality	Image modality.

Returns: Bias field removed from image.

Warning: none.

template<class D >

Vector< size_t > Bial::Brain::COGbyHeadTopDistance	(	const Image< D > &	img,
		const std::string &	orientation
	)

Returns a Vector with COG coordinates, based on intensity weighted values of the image and distance from the top of the head.

Date: 2013/Aug/27

Parameters

img	A brain image.
orientation	Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: Vector with COG coordinates.

Warning: none.

template<class D >

Vector< size_t > Bial::Brain::COGbyIntegralImage	(	const Image< D > &	img,
		const std::string &	orientation,
		MRIModality	modality
	)

Returns a Vector with COG coordinates, based on intensity weighted values of the image and distance from the top of the head.

Date: 2013/Aug/27

Parameters

img	A brain image.
orientation	Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.
modality	Image modality. Defined in Image.hpp.

Returns: Vector with COG coordinates.

Warning: none.

template<class D >

Vector< size_t > Bial::Brain::COGbyIntensityThreshold ( const Image< D > & img )

Returns a Vector with COG coordinates, based on a binary mask of the image main object.

Date: 2013/Aug/27

Parameters

img	A brain image.

Returns: Vector with COG coordinates.

Warning: none.

template<class D >

Vector< size_t > Bial::Brain::COGbyWeightedIntensity ( const Image< D > & img )

Returns a Vector with COG coordinates, based on intensity weighted values of the image.

Date: 2013/Aug/27

Parameters

img	A brain image.

Returns: Vector with COG coordinates.

Warning: none.

template<class D >

size_t Bial::Brain::HeadTopSlice	(	const Image< D > &	img,
		const std::string &	orientation
	)

It searches for the first superior axial slice with a pixel which intensity is higher than otsu threshold.

Date: 2013/Aug/27

Parameters

img	A brain image.
orientation	Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: The slice of the first slice in axial orientation that contains pixels from the top of the head.

Warning: none.

template<class D >

Image< D > Bial::Brain::InhomogeneityCorrection	(	const Image< D > &	img,
		const Image< D > &	msk,
		float	radius = `15.5`,
		size_t	compression = `2`,
		MRIModality	modality = `MRIModality::T1`
	)

Computes bias surface based on white matter pixels in the image.

Date: 2014/Jan/08

Parameters

img	A MRI image.
msk	Brain mask.
radius	Radius for distance transform. For searching local WM pixel (7.0 to 28.0)
compression	compression rate to compute bias field faster (1, 2, or 4).
modality	Image modality.

Returns: Image with bias field surface.

Warning: none.

template<class D >

Vector< size_t > Bial::Brain::Location	(	const Image< D > &	img,
		const std::string &	orientation,
		Vector< Box > &	best_rectangles,
		Image< float > &	similarity
	)

Finds the best location of a box inside the brain and of surrounding boxes outside of the brain.

Date: 2014/Oct/30

Parameters

img	A MRI image.
orientation	Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.
best_rectangles	Rectangles containing the brain and external regions.
similarity	Similarity image showing the most probable location of the brain box center.

Returns: The center of gravity of the brain.

Warning: none.

template<class D >

Image< D > Bial::Brain::RemoveIntensityOutliers	(	const Image< D > &	img,
		const Image< D > &	msk,
		float	compression,
		MRIModality	modality
	)

Remove outliers from brain mask which have extreme intensity values. Used to correct inhomogeneity.

Date: 2014/Jan/07

Parameters

img	An MRI image of the head.
msk	Brain mask.
compression	compression rate to compute bias field faster (1, 2, or 4).
modality	Image modality. Defined in Image.hpp. Must be MRI_T1, MRI_T2, or MRI_PD.

Returns: Brain mask without outliers.

Warning: none.

template<class D >

Image< D > Bial::Brain::SkullStripping	(	const Image< D > &	img,
		const std::string &	orientation
	)

Segments the brain from the background.

Date: 2014/Oct/30

Parameters

img	A MRI image.
orientation	Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: Segmentation of the brain.

Warning: none.

template<class D >

void Bial::Brain::TissueLabeling	(	const Image< D > &	image,
		const Image< D > &	mask,
		Image< int > &	label,
		D	intensity
	)

Set labeled clusters into low and high intensity tissues. Low intensity tissue pixels have their label set to 0 and high intensity tissue pixels have their label set to 1.

Date: 2013/Sep/04

Parameters

image	An MRI image of the head.
mask	Brain or tissue mask.
label	Brain or tissues segmented in labeled clusters.
intensity	Threshold between low and high intensity tissues.

Returns: none.

Warning: none.

template<class D >

Image< int > Bial::Brain::TissueSegmentation	(	const Image< D > &	img,
		const Image< D > &	msk,
		D	tissue_intensity,
		float	scl_min,
		float	scl_max,
		bool	hierarchical
	)

Set labeled clusters into low and high intensity tissues. Low intensity tissue pixels have their label set to 0 and high intensity tissue pixels have their label set to 1.

Date: 2013/Sep/04

Parameters

img	An MRI image of the head.
msk	Brain mask.
tissue_intensity	Value between low and high intensity tissues.
scl_min,scl_max	Minimum and maximum number of neighbers for OPF clustering.
hierarchical	Selects between spectral (false) or hierarchicar clustering.

Returns: none.

Warning: none.

template<class D >

Image< int > Bial::Brain::TissueSegmentation	(	const Image< D > &	img,
		const Image< D > &	msk,
		MRIModality	modality,
		float	csf_scl_min = `0.1`,
		float	csf_scl_max = `0.2`,
		float	gm_scl_min = `0.2`,
		float	gm_scl_max = `0.3`,
		bool	hierarchical = `false`
	)

Segment brain into CSF, GM, and WM tissues.

Date: 2013/Sep/04

Parameters

img	An MRI image of the head.
msk	Brain mask.
modality	Image modality. Defined in Image.hpp. Must be MRI_T1, MRI_T2, or MRI_PD.
xxx_scl_min,xxx_scl_max	Minimum and maximum number of neighbers for OPF clustering to segment xxx tissue.
hierarchical	Selects between spectral (false) or hierarchicar clustering.

Returns: none.

Warning: none.

Classes

Functions

Function Documentation