fslio.c File Reference

Main collection of FSL i/o routines, written by Mark Jenkinson, FMRIB. More...

#include "fslio.h"
#include "assert.h"

Include dependency graph for fslio.c:

Macros
#define	FSLIOERR(x)

Functions
const char *	FslFileTypeString (int filetype)
	Return a string describing the format of the dataset.
int	FslIsValidFileType (int filetype)
int	FslBaseFileType (int filetype)
int	FslGetFileType2 (const FSLIO *fslio, int quiet)
int	FslGetFileType (const FSLIO *fslio)
void	FslSetFileType (FSLIO *fslio, int filetype)
int	FslIsSingleFileType (int filetype)
int	FslIsCompressedFileType (int filetype)
int	FslGetWriteMode (const FSLIO *fslio)
void	FslSetWriteMode (FSLIO *fslio, int mode)
int	FslGetEnvOutputType (void)
int	FslFileType (const char *fname)
int	FslGetReadFileType (const FSLIO *fslio)
	return the best estimate of the true file type
int	FslFileExists (const char *filename)
char *	FslMakeBaseName (const char *fname)
void	FslGetHdrImgNames (const char *filename, const FSLIO *fslio, char **hdrname, char **imgname)
FSLIO *	FslInit (void)
	allocate space for the FSLIO struct and set some sensible defaults
void	FslSetInit (FSLIO *fslio)
void	FslInit4Write (FSLIO *fslio, const char *filename, int ft)
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	FslCloneHeader (FSLIO *dest, const FSLIO *src)
int	fsl_fileexists (const char *fname)
int	FslCheckForMultipleFileNames (const char *filename)
int	check_for_multiple_filenames (const char *filename)
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.
void *	FslReadAllVolumes (FSLIO *fslio, char *filename)
	Read the header and all data into the FSLIO structure.
size_t	FslReadVolumes (FSLIO *fslio, void *buffer, size_t nvols)
	Read the first nvols Volumes from a 4D dataset.
void	FslWriteAllVolumes (FSLIO *fslio, const void *buffer)
	Writes all data from buffer (using size info from fslio) to file.
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.
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.
int	FslSeekVolume (FSLIO *fslio, size_t vols)
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	FslSetVoxUnits (FSLIO *fslio, const char *units)
void	FslGetVoxUnits (FSLIO *fslio, char *units)
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)
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)
void	FslSetStdXform (FSLIO *fslio, short sform_code, mat44 stdmat)
short	FslGetStdXform (FSLIO *fslio, mat44 *stdmat)
void	FslSetRigidXform (FSLIO *fslio, short qform_code, mat44 rigidmat)
short	FslGetRigidXform (FSLIO *fslio, mat44 *rigidmat)
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)
void	FslSetIntensityScaling (FSLIO *fslio, float slope, float intercept)
int	FslGetIntensityScaling (FSLIO *fslio, float *slope, float *intercept)
mat33	mat44_to_mat33 (mat44 x)
int	FslGetLeftRightOrder (FSLIO *fslio)
void	FslSetAnalyzeSform (FSLIO *fslio, const short *orig, float dx, float dy, float dz)
void	FslGetAnalyzeOrigin (FSLIO *fslio, short orig[5])
int	FslClose (FSLIO *fslio)
	Write header and image data if this dataset was open for writing. Close the dataset header and data files.
void	AvwSwapHeader (struct dsr *avw)
int	FslReadRawHeader (void *buffer, const char *filename)
void	FslSetOverrideOutputType (int type)
int	FslGetOverrideOutputType (void)
void	FslSetIgnoreMFQ (int flag)
int	FslGetIgnoreMFQ (void)
FSLIO *	FslReadHeader (char *fname)
	Reads nifti/anz header, no data is read.
double ***	FslGetVolumeAsScaledDouble (FSLIO *fslio, int vol)
	Return volume #vol (0-based) as a 3D array of scaled doubles.
double ****	FslGetBufferAsScaledDouble (FSLIO *fslio)
	Return the fslio data buffer of a 1-4D dataset as a 4D 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 ***	d3matrix (int zh, int yh, int xh)
	allocate a 3D 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

Detailed Description

Main collection of FSL i/o routines, written by Mark Jenkinson, FMRIB.

• updates by Rick Reynolds, SSCC, NIMH

Macro Definition Documentation

FSLIOERR

#define FSLIOERR

(

x

)

Value:

{ fprintf(stderr,"Error:: %s\n",(x)); fflush(stderr); exit(EXIT_FAILURE); }

Function Documentation

FslGetReadFileType()

int FslGetReadFileType

(

const FSLIO *

fslio

)

return the best estimate of the true file type

This function is used to return the best estimate of the true file type once a simple open has occurred - for now it is used after a nifti open call is made

Parameters

fslio

data structure

Returns

FSL_TYPE filetype code

See also

FSL_TYPE