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fslio.h File Reference

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"

Go to the source code of this file.

Compounds
struct	FSLIO
Defines
#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)
FSLIO*	FslXOpen (const char *filename,const char *opts,int filetype)
int	FslSeekVolume (FSLIO *fslio,size_t vols)
int	FslClose (FSLIO *fslio)
void*	FslReadAllVolumes (FSLIO *fslio,char *filename)
void	FslWriteAllVolumes (FSLIO *fslio,const void *buffer)
size_t	FslReadVolumes (FSLIO *fslio,void *buffer,size_t nvols)
size_t	FslWriteVolumes (FSLIO *fslio,const void *buffer,size_t nvols)
void	FslWriteHeader (FSLIO *fslio)
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)
char*	FslFileTypeString (int filetype)
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)
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,const char *units)
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)
size_t	FslReadRowSeries (FSLIO *fslio,void *buffer,short row,short slice,size_t nvols)
size_t	FslReadTimeSeries (FSLIO *fslio,void *buffer,short xVox,short yVox,short zVox,size_t nvols)
mat33	mat44_to_mat33 (mat44 x)
FSLIO*	FslReadHeader (char *fname)
double****	FslGetBufferAsScaledDouble (FSLIO *fslio)
double***	FslGetVolumeAsScaledDouble (FSLIO *fslio,int vol)
int	convertBufferToScaledDouble (double *outbuf,void *inbuf,long len,float slope,float inter,int nifti_datatype)
double****	d4matrix (int th,int zh,int yh,int xh)
double***	d3matrix (int zh,int yh,int xh)

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Detailed Description

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

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Function Documentation

void AvwSwapHeader ( struct dsr * avw )

----- if writing the image, need to worry about the header bit ----- *

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