Class that defines how to read Bruker file format. Bruker IMAGE FILE FORMAT - The following is a brief description of the Bruker file format taken from: More...

#include <itkBruker2DSEQImageIO.h>

Inheritance diagram for itk::Bruker2DSEQImageIO:

Collaboration diagram for itk::Bruker2DSEQImageIO:

List of all members.

Public Types
typedef VectorContainer < unsigned int, double >	ACQEchoTimeContainerType
typedef VectorContainer < unsigned int, double >	ACQInversionTimeContainerType
typedef VectorContainer < unsigned int, double >	ACQRepetitionTimeContainerType
typedef VectorContainer < unsigned int, double >	ACQSliceSepnContainerType
typedef SmartPointer< Self >	Pointer
typedef VectorContainer < unsigned int, double >	RECOFOVContainerType
typedef VectorContainer < unsigned int, int >	RECOTranspositionContainerType
typedef Bruker2DSEQImageIO	Self
typedef ImageIOBase	Superclass
typedef ImageIOBase	SuperClass
Public Member Functions
virtual bool	CanReadFile (const char *FileNameToRead)
virtual bool	CanWriteFile (const char *)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual const char *	GetNameOfClass () const
virtual void	Read (void *buffer)
virtual void	ReadImageInformation ()
virtual void	Write (const void *)
virtual void	WriteImageInformation ()
Static Public Member Functions
static Pointer	New ()
Protected Member Functions
	Bruker2DSEQImageIO ()
void	PrintSelf (std::ostream &os, Indent indent) const
	~Bruker2DSEQImageIO ()
Private Member Functions
	Bruker2DSEQImageIO (const Self &)
void	operator= (const Self &)
void	SwapBytesIfNecessary (void *buffer, SizeValueType numberOfPixels)
Private Attributes
ImageIOBase::ByteOrder	m_MachineByteOrder

Detailed Description

Class that defines how to read Bruker file format. Bruker IMAGE FILE FORMAT - The following is a brief description of the Bruker file format taken from:

Author:: Don C. Bigler http://www.mrc-cbu.cam.ac.uk/Imaging/Common/brukerformat.shtml.

For the Bruker format, a single scanning session is stored in its own directory. The directory is named according to the subject name or number, as typed in by the scanner operator. The directory name usually specifies the subject name/number and which session this is for that subject. Thus, a typical directory name would be

010005-m00.5X1

where '010005' is the WBIC subject number of the subject, the 00 of 'm00' means this is the first scanning session that subject number of the session for that subject, on that day (1). The first two letters specify the day, since some arbitrary base date - set in the Bruker software.

The WBIC number (e.g. 010005) in turn is made up of the year the subject was first scanned (01 = 2001) and where that subject is in the sequence of new numbers allocated (5 = 5th subject in the year 2001 who has needed a new subject number).

Within the session directory (e.g 010005-m00.5X1), there are: 1. a text file, named 'subject' 2. A subdirectory numbered 1, 2, 3 etc, for each saved run of data acquisition in that session

Within each of the run directories (e.g. 010005-m00.5X1/5) there are the following: 1. an 'imnd' or 'method' text file, containing parameters used in setting up and acquiring the data from the scanner 2. an 'acqp' (ACquisition Parameter) text file, with further details of the acquisition parameters used for that run 3. a large 'fid' file, that contains the raw, unreconstructed MR Free Induction Decay data 4. a subdirectory 'pdata' (Processed Data), that contains any reconstructions of the data into images 5. various other files, including the 'pulseprogram' and 'grdprog.r' gradient programs

Within each of the 'pdata' subdirectories (e.g 01001-m00.5X1/5/pdata), there are numbered subdirectories (1,2,3 etc) for each new reconstruction of the raw data into images. There is usually only one such reconstruction, in subdirectory '1'.

Within each reconstruction directory (e.g 01001-m00.5X1/5/pdata/1), there are: 1. a '2dseq' file. This is the 3D (structural etc) or 4D (FMRI) image file. It is simply a binary block of data, which could simply be renamed as 'myscan.img' to make an acceptable Analyze .img file. 2. a 'reco' text file, containing some details of the reconstruction. 3. a 'meta' text file, which I think contains information for the display of the 2dseq file within ParaVision. 4. a 'd3proc' file, containing image size definition parameters, inter alia.

The 'reco', 'acqp', 'd3proc', and '2dseq' files are required for this reader. It will look for these files in the directory structure described above. The path and filename of the '2dseq' file must be the name of the file to read (see CanReadFile). This class supports reading only.

Definition at line 113 of file itkBruker2DSEQImageIO.h.

Member Typedef Documentation

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQEchoTimeContainerType

Definition at line 132 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQInversionTimeContainerType

Definition at line 134 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQRepetitionTimeContainerType

Definition at line 133 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQSliceSepnContainerType

Definition at line 135 of file itkBruker2DSEQImageIO.h.

typedef SmartPointer< Self > itk::Bruker2DSEQImageIO::Pointer

Reimplemented from itk::ImageIOBase.

Definition at line 121 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::RECOFOVContainerType

Special types used for Bruker meta data.

Definition at line 127 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, int > itk::Bruker2DSEQImageIO::RECOTranspositionContainerType

Definition at line 131 of file itkBruker2DSEQImageIO.h.

typedef Bruker2DSEQImageIO itk::Bruker2DSEQImageIO::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

Definition at line 119 of file itkBruker2DSEQImageIO.h.

typedef ImageIOBase itk::Bruker2DSEQImageIO::Superclass

Reimplemented from itk::ImageIOBase.

Definition at line 120 of file itkBruker2DSEQImageIO.h.

typedef ImageIOBase itk::Bruker2DSEQImageIO::SuperClass

Definition at line 116 of file itkBruker2DSEQImageIO.h.

Constructor & Destructor Documentation

itk::Bruker2DSEQImageIO::Bruker2DSEQImageIO ( ) [protected]

itk::Bruker2DSEQImageIO::~Bruker2DSEQImageIO ( ) [protected]

itk::Bruker2DSEQImageIO::Bruker2DSEQImageIO ( const Self & ) [private]

Member Function Documentation

virtual bool itk::Bruker2DSEQImageIO::CanReadFile ( const char * FileNameToRead ) [virtual]

Determine if the file can be read with this ImageIO implementation.

Author:: Don C. Bigler

Parameters:

FileNameToRead The name of the file to test for reading.

Returns:: Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::Bruker2DSEQImageIO::CanWriteFile ( const char * ) [inline, virtual]

Determine if the file can be written with this ImageIO implementation. FileNameToWrite The name of the file to test for writing.

Author:: Don C. Bigler

Postcondition:: This function will always return false (Not implemented).

Returns:: Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

Definition at line 160 of file itkBruker2DSEQImageIO.h.

virtual::itk::LightObject::Pointer itk::Bruker2DSEQImageIO::CreateAnother ( void ) const [virtual]

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::LightProcessObject.

virtual const char* itk::Bruker2DSEQImageIO::GetNameOfClass ( ) const [virtual]

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

static Pointer itk::Bruker2DSEQImageIO::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

void itk::Bruker2DSEQImageIO::operator= ( const Self & ) [private]

This method causes the filter to generate its output.

Reimplemented from itk::ImageIOBase.

void itk::Bruker2DSEQImageIO::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const `[protected, virtual]`

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageIOBase.

virtual void itk::Bruker2DSEQImageIO::Read ( void * buffer ) [virtual]

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::Bruker2DSEQImageIO::ReadImageInformation ( ) [virtual]

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.