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fslio.c File Reference

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

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

Defines

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

Functions

char* FslFileTypeString (int filetype)

Return a string describing the format of the dataset. More...

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. More...

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. More...

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,const char *units)

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. More...

FSLIO* FslXOpen (const char *filename,const char *opts,int filetype)

Opens a file for either reading or writing. More...

void* FslReadAllVolumes (FSLIO *fslio,char *filename)

Read the header and all data into the FSLIO structure. More...

size_t FslReadVolumes (FSLIO *fslio,void *buffer,size_t nvols)

Read the first nvols Volumes from a 4D dataset. More...

void FslWriteAllVolumes (FSLIO *fslio,const void *buffer)

Writes all data from buffer (using size info from fslio) to file. More...

size_t FslWriteVolumes (FSLIO *fslio,const void *buffer,size_t nvols)

Write the first nvols volumes in buffer to disk. More...

void FslWriteHeader (FSLIO *fslio)

Writes nifti/anz header and opens img file ready for writing. More...

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. More...

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. More...

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. More...

size_t FslReadCplxVolumes (FSLIO *fslio,void *buffer,size_t nvols,char mode)

size_t FslWriteCplxVolumes (FSLIO *fslio,void *buffer,size_t nvols,char mode)

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. More...

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. More...

double*** FslGetVolumeAsScaledDouble (FSLIO *fslio,int vol)

Return volume vol (0-based) as a 3D array of scaled doubles. More...

double**** FslGetBufferAsScaledDouble (FSLIO *fslio)

Return the fslio data buffer of a 1-4D dataset as a 4D array of scaled doubles. More...

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. More...

double*** d3matrix (int zh,int yh,int xh)

allocate a 3D buffer, use 1 contiguous buffer for the data. More...

double**** d4matrix (int th,int zh,int yh,int xh)

allocate a 4D buffer, use 1 contiguous buffer for the data. More...

Detailed Description

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

- updates by Rick Reynolds, SSCC, NIMH

Function Documentation

void AvwSwapHeader ( struct dsr * avw )

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

int FslClose ( FSLIO * fslio )

Write header and image data if this dataset was open for writing. Close the dataset header and data files.

Parameters:

fslio pointer to FSLIO data structure

Returns:
-1 on error, 0 OK ???.

char * FslFileTypeString ( int filetype )

Return a string describing the format of the dataset.

Parameters:

filetype FSL data format code. Legal values are as defined by FSL_TYPE.

Returns:
A string with the data format name, e.g. "ANALYZE-7.5"
See also:
FSL_TYPE

double **** FslGetBufferAsScaledDouble ( FSLIO * fslio )

Return the fslio data buffer of a 1-4D dataset as a 4D array of scaled doubles.
Array is indexed as buf[0..tdim-1][0..zdim-1][0..ydim-1][0..xdim-1].
The array will be byteswapped to native-endian.
Array values are scaled as per fslio header slope and intercept fields.
Parameters:

fslio pointer to open dataset

Returns:
Pointer to 4D double array, NULL on error

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

double *** FslGetVolumeAsScaledDouble ( FSLIO * fslio,

int vol )

Return volume vol (0-based) as a 3D array of scaled doubles.
Volume Array is indexed as [0..zdim-1][0..ydim-1][0..xdim-1].
The array will be byteswapped to native-endian.
Array values are scaled as per fslio header slope and intercept fields.
Parameters:

fslio pointer to open dataset

vol volume number to read (legal range [0..tdim-1])

Returns:
Pointer to 3D double array, NULL on error

FSLIO * FslInit ( void )

allocate space for the FSLIO struct and set some sensible defaults.

Returns:
A pointer to an initialized FSLIO data structure

FSLIO * FslOpen ( const char * filename,

const char * opts )

Opens a file for either reading or writing.
The format of the output dataset is determined automatically by passing filetype -1 to FslXOpen.
See also:
FslXOpen

void * FslReadAllVolumes ( FSLIO * fslio,

char * filename )

Read the header and all data into the FSLIO structure.
There is no need for FslOpen or FslClose calls when FslReadAllVolumes() is called.
This routine allocates the buffer to hold the entire dataset.
The data block returned will contain the data in whatever datatype it is stored as on disk (therefore it is a void *).
The data buffer will be byteswapped to native-endian.
The data buffer will not be scaled.
The best call to make before this is FslInit() or a calloc() for fslio. (??? why calloc if this allocates the buffer ???)
Parameters:

fslio pointer to an open dataset

filename Name of the dataset to read.

Returns:
A pointer to the data block buffer (allocated by this function).
Return Null on error ??? is this true ???

Note this pointer is also in the FSLIO structure as fslio->niftiptr->data.
Note a void pointer is returned, as the datablock is of variable datatype.

FSLIO * FslReadHeader ( char * fname )

Reads nifti/anz header, no data is read.

Parameters:

fname filename specification (could be .img,.hdr,.nii, or no ext

Returns:
FSLIO data structure with the nifti_image structure fields filled as per fname header. NULL on error

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.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: filepointer in file data array is restored to its initial position.
Parameters:

fslio pointer to open dataset

buffer buffer to hold one row from each volume.

row row number (0 based) to read [0 y-1]

slice slice number (0 based) to read

nvols number of volumes to read a row from

Returns:
Number of volumes from which a row was successfully read. 0 on error.

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.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: filepointer in file data array is restored to its initial position.
Parameters:

fslio pointer to open dataset

buffer buffer large enough to hold 1 slice from each volume

slice slice number (0 based) to read [0 z-1]

nvols number of volumes to read a slice from

Returns:
Number of volumes from which a slice was successfully read. 0 on error.

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.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: filepointer in file data array is restored to its initial position.
Parameters:

fslio pointer to open dataset

buffer buffer to hold one timeseries vector

xVox x voxel [0 x-1]

yVox y voxel [0 y-1]

zVox z voxel [0 z-1]

nvols number of volumes to read a voxel from

Returns:
Number of volumes from which a voxel was successfully read. 0 on error.

size_t FslReadVolumes ( FSLIO * fslio,

void * buffer,

size_t nvols )

Read the first nvols Volumes from a 4D dataset.

Parameters:

fslio pointer to open dataset

buffer buffer to read data into, allocated by ???

nvols number of volumes to read

Returns:
Number of volumes read.

void FslWriteAllVolumes ( FSLIO * fslio,

const void * buffer )

Writes all data from buffer (using size info from fslio) to file.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: If file format is Analyze (not nifti) and in Neurological order then SWAP DATA into Radiological order.
Parameters:

fslio pointer to open dataset

buffer pointer to data array. Size and datatype of this buffer

void FslWriteHeader ( FSLIO * fslio )

Writes nifti/anz header and opens img file ready for writing.

Parameters:

fslio pointer to open dataset

size_t FslWriteVolumes ( FSLIO * fslio,

const void * buffer,

size_t nvols )

Write the first nvols volumes in buffer to disk.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: If file format is Analyze (not nifti) and in Neurological order then SWAP DATA into Radiological order.
Parameters:

fslio pointer to open dataset

buffer pointer to data array. Size and datatype of this buffer

nvols number of volumes to write

Returns:
??? looks like return of retval is missing ??? 0 on error.

FSLIO * FslXOpen ( const char * filename,

const char * opts,

int filetype )

Opens a file for either reading or writing.
Files to be read are automatically read whether compressed or not. Also, reading uses the file extension and will fail if that file does not exist. For a more robust read, pass the basename in as then all types will be tried.
Parameters:

filename Name (or basename) of the file to open

opts Flags for fopen() of dataset, eg "r", "wb", etc.

filetype specifies the type of file to be written. Legal values are as defined by FSL_TYPE. If filetype is less than zero, then it is ignored and the type is determined by the filename extension or, failing that, the environment default.

Returns:
pointer to FSLIO dataset datastructure
See also:
FSLIO , FSL_TYPE

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.
Array is indexed as buf[0..th-1][0..zh-1][0..yh-1][0..xh-1].
To access all elements as a vector, use buf[0][0][0][i] where i can range from 0 to th*zh*yh*xh - 1.
Parameters:

outbuf pointer to array of doubles of size len

inbuf void pointer to an array of len items of datatype nifti_datatype

len number of elements in outbuf and inbuf

slope slope term of scaling to be applied

inter intercept term of scaling to be applied: out = (in*slope)+inter

nifti_datatype NIFTI datatype code for the datatype of the elements in inbuf

Returns:
error code: 0=OK -1=error

double *** d3matrix ( int zh,

int yh,

int xh )

allocate a 3D buffer, use 1 contiguous buffer for the data.
Array is indexed as buf[0..zh][0..yh][0..xh].
To access all elements as a vector, use buf[0][0][i] where i can range from 0 to zh*yh*xh - 1. Adaptation of Numerical Recipes in C nrutil.c allocation routines.
Parameters:

zh slowest changing dimension

yh 2nd fastest changing dimension

xh fastest changing dimension

Returns:
Pointer to 3D double array

double **** d4matrix ( int th,

int zh,

int yh,

int xh )

allocate a 4D buffer, use 1 contiguous buffer for the data.
Array is indexed as buf[0..th][0..zh][0..yh][0..xh].
To access all elements as a vector, use buf[0][0][0][i] where i can range from 0 to th*zh*yh*xh - 1. Adaptation of Numerical Recipes in C nrutil.c allocation routines.
Parameters:

th slowest changing dimension

zh 2nd slowest changing dimension

yh 2nd fastest changing dimension

xh fastest changing dimension

Returns:
Pointer to 4D double array

Generated at Thu Aug 28 16:47:55 2008 for nifti1_io by

Defines
#define	FSLIOERR(x) { fprintf(stderr,"Error:: %s\n",(x)); fflush(stderr); exit(EXIT_FAILURE); }
Functions
char*	FslFileTypeString (int filetype)
	Return a string describing the format of the dataset. More...
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. More...
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. More...
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,const char units)
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. More...
FSLIO*	FslXOpen (const char filename,const char opts,int filetype)
	Opens a file for either reading or writing. More...
void*	FslReadAllVolumes (FSLIO fslio,char filename)
	Read the header and all data into the FSLIO structure. More...
size_t	FslReadVolumes (FSLIO fslio,void buffer,size_t nvols)
	Read the first nvols Volumes from a 4D dataset. More...
void	FslWriteAllVolumes (FSLIO fslio,const void buffer)
	Writes all data from buffer (using size info from fslio) to file. More...
size_t	FslWriteVolumes (FSLIO fslio,const void buffer,size_t nvols)
	Write the first nvols volumes in buffer to disk. More...
void	FslWriteHeader (FSLIO *fslio)
	Writes nifti/anz header and opens img file ready for writing. More...
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. More...
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. More...
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. More...
size_t	FslReadCplxVolumes (FSLIO fslio,void buffer,size_t nvols,char mode)
size_t	FslWriteCplxVolumes (FSLIO fslio,void buffer,size_t nvols,char mode)
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. More...
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. More...
double***	FslGetVolumeAsScaledDouble (FSLIO *fslio,int vol)
	Return volume vol (0-based) as a 3D array of scaled doubles. More...
double****	FslGetBufferAsScaledDouble (FSLIO *fslio)
	Return the fslio data buffer of a 1-4D dataset as a 4D array of scaled doubles. More...
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. More...
double***	d3matrix (int zh,int yh,int xh)
	allocate a 3D buffer, use 1 contiguous buffer for the data. More...
double****	d4matrix (int th,int zh,int yh,int xh)
	allocate a 4D buffer, use 1 contiguous buffer for the data. More...