Data structures for using the fslio API. Written by Mark Jenkinson, FMRIB. More...

#include <stdio.h>
#include <nifti1_io.h>
#include <znzlib.h>
#include "dbh.h"

Include dependency graph for fslio.h:

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Classes
struct	FSLIO
	High level data structure for open datasets in the fslio API. More...

Macros
#define	FSL_TYPE_ANALYZE 0
#define	FSL_TYPE_NIFTI 1
#define	FSL_TYPE_NIFTI_PAIR 2
#define	FSL_TYPE_MINC 4
#define	FSL_TYPE_ANALYZE_GZ 100
#define	FSL_TYPE_NIFTI_GZ 101
#define	FSL_TYPE_NIFTI_PAIR_GZ 102
#define	FSL_TYPE_MINC_GZ 104
#define	FSL_RADIOLOGICAL -1
#define	FSL_NEUROLOGICAL 1

Typedefs
typedef unsigned char	THIS_UINT8
typedef char	THIS_INT8
typedef unsigned short	THIS_UINT16
typedef short	THIS_INT16
typedef unsigned int	THIS_UINT32
typedef int	THIS_INT32
typedef unsigned long	THIS_UINT64
typedef long	THIS_INT64
typedef float	THIS_FLOAT32
typedef double	THIS_FLOAT64

Functions
FSLIO *	FslOpen (const char filename, const char opts)
	Opens a file for either reading or writing.
FSLIO *	FslXOpen (const char filename, const char opts, int filetype)
	Opens a file for either reading or writing.
int	FslSeekVolume (FSLIO *fslio, size_t vols)
int	FslClose (FSLIO *fslio)
	Write header and image data if this dataset was open for writing. Close the dataset header and data files.
void *	FslReadAllVolumes (FSLIO fslio, char filename)
	Read the header and all data into the FSLIO structure.
void	FslWriteAllVolumes (FSLIO fslio, const void buffer)
	Writes all data from buffer (using size info from fslio) to file.
size_t	FslReadVolumes (FSLIO fslio, void buffer, size_t nvols)
	Read the first nvols Volumes from a 4D dataset.
size_t	FslWriteVolumes (FSLIO fslio, const void buffer, size_t nvols)
	Write the first nvols volumes in buffer to disk.
void	FslWriteHeader (FSLIO *fslio)
	Writes nifti/anz header and opens img file ready for writing.
int	FslFileExists (const char *filename)
char *	FslMakeBaseName (const char *fname)
int	FslCheckForMultipleFileNames (const char *filename)
int	FslGetEnvOutputType (void)
void	FslSetIgnoreMFQ (int flag)
int	FslGetIgnoreMFQ (void)
void	FslSetOverrideOutputType (int type)
int	FslGetOverrideOutputType (void)
int	FslGetFileType (const FSLIO *fslio)
void	FslSetFileType (FSLIO *fslio, int filetype)
int	FslIsSingleFileType (int filetype)
int	FslIsCompressedFileType (int filetype)
int	FslBaseFileType (int filetype)
const char *	FslFileTypeString (int filetype)
	Return a string describing the format of the dataset.
int	FslGetWriteMode (const FSLIO *fslio)
void	FslSetWriteMode (FSLIO *fslio, int mode)
void	AvwSwapHeader (struct dsr *avw)
int	FslReadRawHeader (void buffer, const char filename)
FSLIO *	FslInit (void)
	allocate space for the FSLIO struct and set some sensible defaults
void	FslInitHeader (FSLIO *fslio, short t, size_t x, size_t y, size_t z, size_t v, float vx, float vy, float vz, float tr, size_t dim)
void	FslSetInit (FSLIO *fslio)
void	FslCloneHeader (FSLIO dest, const FSLIO src)
size_t	FslGetVolSize (FSLIO *fslio)
void	FslSetDim (FSLIO *fslio, short x, short y, short z, short v)
void	FslGetDim (FSLIO fslio, short x, short y, short z, short *v)
void	FslSetDimensionality (FSLIO *fslio, size_t dim)
void	FslGetDimensionality (FSLIO fslio, size_t dim)
void	FslSetVoxDim (FSLIO *fslio, float x, float y, float z, float tr)
void	FslGetVoxDim (FSLIO fslio, float x, float y, float z, float *tr)
void	FslGetCalMinMax (FSLIO fslio, float min, float *max)
void	FslSetCalMinMax (FSLIO *fslio, float min, float max)
void	FslGetAuxFile (FSLIO fslio, char aux_file)
void	FslSetAuxFile (FSLIO fslio, const char aux_file)
void	FslSetTimeUnits (FSLIO fslio, const char units)
void	FslGetTimeUnits (FSLIO fslio, char units)
void	FslSetDataType (FSLIO *fslio, short t)
size_t	FslGetDataType (FSLIO fslio, short t)
int	FslGetIntensityScaling (FSLIO fslio, float slope, float *intercept)
void	FslSetIntent (FSLIO *fslio, short intent_code, float p1, float p2, float p3)
short	FslGetIntent (FSLIO fslio, short intent_code, float p1, float p2, float *p3)
short	FslGetStdXform (FSLIO fslio, mat44 stdmat)
void	FslSetStdXform (FSLIO *fslio, short sform_code, mat44 stdmat)
void	FslGetMMCoord (mat44 stdmat, float voxx, float voxy, float voxz, float mmx, float mmy, float *mmz)
void	FslGetVoxCoord (mat44 stdmat, float mmx, float mmy, float mmz, float voxx, float voxy, float *voxz)
short	FslGetRigidXform (FSLIO fslio, mat44 rigidmat)
void	FslSetRigidXform (FSLIO *fslio, short qform_code, mat44 rigidmat)
int	FslGetLeftRightOrder (FSLIO *fslio)
void	FslSetAnalyzeSform (FSLIO fslio, const short orig, float dx, float dy, float dz)
void	FslGetAnalyzeOrigin (FSLIO *fslio, short orig[5])
size_t	FslReadSliceSeries (FSLIO fslio, void buffer, short slice, size_t nvols)
	Read one slice from each of the first nvols volumes in the dataset, ie get an xyt buffer.
size_t	FslReadRowSeries (FSLIO fslio, void buffer, short row, short slice, size_t nvols)
	Read one row from one slice for first nvols volumes in dataset; ie get an xt buffer.
size_t	FslReadTimeSeries (FSLIO fslio, void buffer, short xVox, short yVox, short zVox, size_t nvols)
	Read one voxel (xyz location) from first nvols volumes in dataset; ie get a t dim buffer.
mat33	mat44_to_mat33 (mat44 x)
FSLIO *	FslReadHeader (char *fname)
	Reads nifti/anz header, no data is read.
double ****	FslGetBufferAsScaledDouble (FSLIO *fslio)
	Return the fslio data buffer of a 1-4D dataset as a 4D array of scaled doubles.
double ***	FslGetVolumeAsScaledDouble (FSLIO *fslio, int vol)
	Return volume #vol (0-based) as a 3D array of scaled doubles.
int	convertBufferToScaledDouble (double outbuf, void inbuf, long len, float slope, float inter, int nifti_datatype)
	allocate a 4D buffer, use 1 contiguous buffer for the data
double ****	d4matrix (int th, int zh, int yh, int xh)
	allocate a 4D buffer, use 1 contiguous buffer for the data
double ***	d3matrix (int zh, int yh, int xh)
	allocate a 3D buffer, use 1 contiguous buffer for the data

Detailed Description

Data structures for using the fslio API. Written by Mark Jenkinson, FMRIB.

Classes

Macros

Typedefs

Functions

Detailed Description