Classes

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

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)
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)
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, 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)
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

int convertBufferToScaledDouble (double *outbuf, void *inbuf, longlen, floatslope, floatinter, intnifti_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:

Returns:

fill the buffer

double*** d3matrix (intzh, intyh, intxh)

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:

Returns:

allocate pointers to slices

allocate pointers for ydim

allocate the data blob

point everything to the data blob

double**** d4matrix (intth, intzh, intyh, intxh)

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:

Returns:

allocate pointers to vols

allocate pointers to slices

allocate pointers for ydim

allocate the data blob

point everything to the data blob

int FslClose (FSLIO *fslio)

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

Returns:

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

char* FslFileTypeString (intfiletype)

Return a string describing the format of the dataset. Parameters:

Returns:

See also:

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:

Returns:

allocate new 4D buffer

cvt it

double*** FslGetVolumeAsScaledDouble (FSLIO *fslio, intvol)

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:

Returns:

allocate new 3D buffer

read in the data in disk format

cvt disk buffer to scaled double buffer

FSLIO* FslInit (void)

allocate space for the FSLIO struct and set some sensible defaults Returns:

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:

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:

Returns:

otherwise it is a nifti file - so read it!

FSLIO* FslReadHeader (char *fname)

Reads nifti/anz header, no data is read. Parameters:

Returns:

get header file name

read header information

size_t FslReadRowSeries (FSLIO *fslio, void *buffer, shortrow, shortslice, size_tnvols)

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:

Returns:

size_t FslReadSliceSeries (FSLIO *fslio, void *buffer, shortslice, size_tnvols)

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:

Returns:

size_t FslReadTimeSeries (FSLIO *fslio, void *buffer, shortxVox, shortyVox, shortzVox, size_tnvols)

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:

Returns:

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

Read the first nvols Volumes from a 4D dataset. Parameters:

Returns:

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:

void FslWriteHeader (FSLIO *fslio)

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

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

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:

Returns:

FSLIO* FslXOpen (const char *filename, const char *opts, intfiletype)

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:

Returns:

See also:

====================== Open file for writing ======================

======================== Open file for reading ======================