tpcnifti.h File Reference

Header file for libtpcnifti. More...

#include "tpcclibConfig.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "tpcextensions.h"
#include "tpcift.h"
#include "tpcfileutil.h"

Go to the source code of this file.

Data Structures
struct	NIFTI_1_HEADER
struct	NIFTI_2_HEADER
struct	NIFTI_EXTENDER
struct	NIFTI_DSR
struct	ANALYZE_HEADER
struct	ANALYZE_DSR

Macros
#define	NIFTI1_HEADER_SIZE   348
#define	NIFTI1_HEADER_EXTENDER_SIZE   4
#define	NIFTI2_HEADER_SIZE   540
#define	NIFTI2_HEADER_EXTENDER_SIZE   4
#define	ANALYZE_HEADER_SIZE   348
#define	NIFTI_UNITS_UNKNOWN   0
#define	NIFTI_UNITS_METER   1
#define	NIFTI_UNITS_MM   2
#define	NIFTI_UNITS_MICRON   4
#define	NIFTI_UNITS_SEC   8
#define	NIFTI_UNITS_MSEC   16
#define	NIFTI_UNITS_USEC   24
#define	NIFTI_UNITS_HERTZ   32
#define	NIFTI_UNITS_PPM   40
#define	NIFTI_UNITS_RADS   48
#define	ANALYZE_DT_NONE   0
#define	ANALYZE_DT_UNKNOWN   0
#define	ANALYZE_DT_BINARY   1
#define	ANALYZE_DT_UNSIGNED_CHAR   2
#define	ANALYZE_DT_SIGNED_SHORT   4
#define	ANALYZE_DT_SIGNED_INT   8
#define	ANALYZE_DT_FLOAT   16
#define	ANALYZE_DT_COMPLEX   32
#define	ANALYZE_DT_DOUBLE   64
#define	ANALYZE_DT_RGB   128
#define	ANALYZE_DT_ALL   255
#define	NIFTI_DT_NONE   ANALYZE_DT_NONE
#define	NIFTI_DT_UNKNOWN   ANALYZE_DT_UNKNOWN
#define	NIFTI_DT_BINARY   ANALYZE_DT_BINARY
#define	NIFTI_DT_UNSIGNED_CHAR   ANALYZE_DT_UNSIGNED_CHAR
#define	NIFTI_DT_SIGNED_SHORT   ANALYZE_DT_SIGNED_SHORT
#define	NIFTI_DT_SIGNED_INT   ANALYZE_DT_SIGNED_INT
#define	NIFTI_DT_FLOAT   ANALYZE_DT_FLOAT
#define	NIFTI_DT_COMPLEX   ANALYZE_DT_COMPLEX
#define	NIFTI_DT_DOUBLE   ANALYZE_DT_DOUBLE
#define	NIFTI_DT_RGB   ANALYZE_DT_RGB
#define	NIFTI_DT_ALL   ANALYZE_DT_ALL
#define	NIFTI_DT_SIGNED_CHAR   256
#define	NIFTI_DT_UNSIGNED_SHORT   512
#define	NIFTI_DT_UNSIGNED_INT   768
#define	NIFTI_DT_LONG_LONG   1024
#define	NIFTI_DT_UNSIGNED_LONG_LONG   1280
#define	NIFTI_DT_LONG_DOUBLE   1536
#define	NIFTI_DT_DOUBLE_PAIR   1792
#define	NIFTI_DT_LONG_DOUBLE_PAIR   2048
#define	NIFTI_DT_RGBA   2304
#define	NIFTI_INTENT_NONE   0
#define	NIFTI_INTENT_CORREL   2
#define	NIFTI_INTENT_TTEST   3
#define	NIFTI_INTENT_FTEST   4
#define	NIFTI_INTENT_ZSCORE   5
#define	NIFTI_INTENT_CHISQ   6
#define	NIFTI_INTENT_BETA   7
#define	NIFTI_INTENT_BINOM   8
#define	NIFTI_INTENT_GAMMA   9
#define	NIFTI_INTENT_POISSON   10
#define	NIFTI_INTENT_NORMAL   11
#define	NIFTI_INTENT_FTEST_NONC   12
#define	NIFTI_INTENT_CHISQ_NONC   13
#define	NIFTI_INTENT_LOGISTIC   14
#define	NIFTI_INTENT_LAPLACE   15
#define	NIFTI_INTENT_UNIFORM   16
#define	NIFTI_INTENT_TTEST_NONC   17
#define	NIFTI_INTENT_WEIBULL   18
#define	NIFTI_INTENT_CHI   19
#define	NIFTI_INTENT_INVGAUSS   20
#define	NIFTI_INTENT_EXTVAL   21
#define	NIFTI_INTENT_PVAL   22
#define	NIFTI_INTENT_LOGPVAL   23
#define	NIFTI_INTENT_LOG10PVAL   24
#define	NIFTI_INTENT_ESTIMATE   1001
#define	NIFTI_INTENT_LABEL   1002
#define	NIFTI_INTENT_NEURONAME   1003
#define	NIFTI_INTENT_GENMATRIX   1004
#define	NIFTI_INTENT_SYMMATRIX   1005
#define	NIFTI_INTENT_DISPVECT   1006
#define	NIFTI_INTENT_VECTOR   1007
#define	NIFTI_INTENT_POINTSET   1008
#define	NIFTI_INTENT_TRIANGLE   1009
#define	NIFTI_INTENT_QUATERNION   1010
#define	NIFTI_INTENT_DIMLESS   1011
#define	NIFTI_XFORM_UNKNOWN   0
#define	NIFTI_XFORM_SCANNER_ANAT   1
#define	NIFTI_XFORM_ALIGNED_ANAT   2
#define	NIFTI_XFORM_TALAIRACH   3
#define	NIFTI_XFORM_MNI_152   4

Functions
void	niftiBasename (char *filename)
int	niftiExists (const char *filename, char *hdrfile, char *imgfile, char *siffile, NIFTI_DSR *header, TPCSTATUS *status)
int	niftiReadHeader (const char *filename, NIFTI_DSR *dsr, int verbose)
int	niftiWriteHeader (const char *filename, NIFTI_DSR *dsr, int verbose)
int	anaExists (const char *filename, char *hdrfile, char *imgfile, char *siffile, ANALYZE_DSR *header, TPCSTATUS *status)
int	anaReadHeader (const char *filename, ANALYZE_DSR *dsr, int verbose)

Detailed Description

Header file for libtpcnifti.

Function are not intended to support all NIfTI and Analyze files or file properties, but only those that have been found necessary in Turku PET Centre. For full NIfTI support, use other libraries, e.g. niftilib http://niftilib.sourceforge.net/

NIfTI-1 and NIfTI-2 documentation and source codes in http://nifti.nimh.nih.gov/

Procedures in this file are not dependent on IMG struct.

Author

Vesa Oikonen

Definition in file tpcnifti.h.

Macro Definition Documentation

ANALYZE_DT_ALL

#define ANALYZE_DT_ALL   255

Analyze 7.5 data type

Definition at line 85 of file tpcnifti.h.

ANALYZE_DT_BINARY

#define ANALYZE_DT_BINARY   1

Analyze 7.5 data type, 1 bit

Definition at line 69 of file tpcnifti.h.

ANALYZE_DT_COMPLEX

#define ANALYZE_DT_COMPLEX   32

Analyze 7.5 data type, 64 bits (two floats)

Definition at line 79 of file tpcnifti.h.

ANALYZE_DT_DOUBLE

#define ANALYZE_DT_DOUBLE   64

Analyze 7.5 data type, 64 bits

Definition at line 81 of file tpcnifti.h.

ANALYZE_DT_FLOAT

#define ANALYZE_DT_FLOAT   16

Analyze 7.5 data type, 32 bits

Definition at line 77 of file tpcnifti.h.

ANALYZE_DT_NONE

#define ANALYZE_DT_NONE   0

Analyze 7.5 data type

Definition at line 65 of file tpcnifti.h.

ANALYZE_DT_RGB

#define ANALYZE_DT_RGB   128

Analyze 7.5 data type

Definition at line 83 of file tpcnifti.h.

ANALYZE_DT_SIGNED_INT

#define ANALYZE_DT_SIGNED_INT   8

Analyze 7.5 data type, 32 bits

Definition at line 75 of file tpcnifti.h.

ANALYZE_DT_SIGNED_SHORT

#define ANALYZE_DT_SIGNED_SHORT   4

Analyze 7.5 data type, 16 bits

Definition at line 73 of file tpcnifti.h.

ANALYZE_DT_UNKNOWN

#define ANALYZE_DT_UNKNOWN   0

Analyze 7.5 data type

Definition at line 67 of file tpcnifti.h.

ANALYZE_DT_UNSIGNED_CHAR

#define ANALYZE_DT_UNSIGNED_CHAR   2

Analyze 7.5 data type, 8 bits

Definition at line 71 of file tpcnifti.h.

ANALYZE_HEADER_SIZE

#define ANALYZE_HEADER_SIZE   348

Analyze header size

Definition at line 41 of file tpcnifti.h.

Referenced by anaReadHeader().

NIFTI1_HEADER_EXTENDER_SIZE

#define NIFTI1_HEADER_EXTENDER_SIZE   4

NIFTI1 header extender size

Definition at line 35 of file tpcnifti.h.

Referenced by imgSetNiftiHeader(), and niftiWriteHeader().

NIFTI1_HEADER_SIZE

#define NIFTI1_HEADER_SIZE   348

NIFTI1 header size

Definition at line 33 of file tpcnifti.h.

Referenced by imgReadNifti(), imgSetNiftiHeader(), niftiReadHeader(), and niftiWriteHeader().

NIFTI2_HEADER_EXTENDER_SIZE

#define NIFTI2_HEADER_EXTENDER_SIZE   4

NIFTI2 header extender size

Definition at line 39 of file tpcnifti.h.

Referenced by imgSetNiftiHeader().

NIFTI2_HEADER_SIZE

#define NIFTI2_HEADER_SIZE   540

NIFTI2 header size

Definition at line 37 of file tpcnifti.h.

Referenced by anaReadHeader(), imgReadNifti(), imgSetNiftiHeader(), niftiReadHeader(), and niftiWriteHeader().

NIFTI_DT_ALL

#define NIFTI_DT_ALL   ANALYZE_DT_ALL

NIFTI1 data type (compatible with Analyze)

Definition at line 108 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_BINARY

#define NIFTI_DT_BINARY   ANALYZE_DT_BINARY

NIFTI1 data type 1 bit (compatible with Analyze)

Definition at line 92 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_COMPLEX

#define NIFTI_DT_COMPLEX   ANALYZE_DT_COMPLEX

NIFTI1 data type 64 bits (compatible with Analyze)

Definition at line 102 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_DOUBLE

#define NIFTI_DT_DOUBLE   ANALYZE_DT_DOUBLE

NIFTI1 data type 64 bits (compatible with Analyze)

Definition at line 104 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_DOUBLE_PAIR

#define NIFTI_DT_DOUBLE_PAIR   1792

NIFTI1 data type 128 bits, complex double

Definition at line 122 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_FLOAT

#define NIFTI_DT_FLOAT   ANALYZE_DT_FLOAT

NIFTI1 data type 32 bits (compatible with Analyze)

Definition at line 100 of file tpcnifti.h.

Referenced by imgReadNifti(), and imgSetNiftiHeader().

NIFTI_DT_LONG_DOUBLE

#define NIFTI_DT_LONG_DOUBLE   1536

NIFTI1 data type 128 bits

Definition at line 120 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_LONG_DOUBLE_PAIR

#define NIFTI_DT_LONG_DOUBLE_PAIR   2048

NIFTI1 data type 256 bits, complex long double

Definition at line 124 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_LONG_LONG

#define NIFTI_DT_LONG_LONG   1024

NIFTI1 data type 64 bits

Definition at line 116 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_NONE

#define NIFTI_DT_NONE   ANALYZE_DT_NONE

NIFTI1 data type (compatible with Analyze)

Definition at line 88 of file tpcnifti.h.

NIFTI_DT_RGB

#define NIFTI_DT_RGB   ANALYZE_DT_RGB

NIFTI1 data type 24 bits (compatible with Analyze)

Definition at line 106 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_RGBA

#define NIFTI_DT_RGBA   2304

NIFTI1 data type 32 bits, 4-byte RGBA

Definition at line 126 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_SIGNED_CHAR

#define NIFTI_DT_SIGNED_CHAR   256

NIFTI1 data type 8 bits

Definition at line 110 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_SIGNED_INT

#define NIFTI_DT_SIGNED_INT   ANALYZE_DT_SIGNED_INT

NIFTI1 data type 32 bits (compatible with Analyze)

Definition at line 98 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_SIGNED_SHORT

#define NIFTI_DT_SIGNED_SHORT   ANALYZE_DT_SIGNED_SHORT

NIFTI1 data type 16 bits (compatible with Analyze)

Definition at line 96 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_UNKNOWN

#define NIFTI_DT_UNKNOWN   ANALYZE_DT_UNKNOWN

NIFTI1 data type (compatible with Analyze)

Definition at line 90 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_UNSIGNED_CHAR

#define NIFTI_DT_UNSIGNED_CHAR   ANALYZE_DT_UNSIGNED_CHAR

NIFTI1 data type 8 bits (compatible with Analyze)

Definition at line 94 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_UNSIGNED_INT

#define NIFTI_DT_UNSIGNED_INT   768

NIFTI1 data type 32 bits

Definition at line 114 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_UNSIGNED_LONG_LONG

#define NIFTI_DT_UNSIGNED_LONG_LONG   1280

NIFTI1 data type 64 bits

Definition at line 118 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_DT_UNSIGNED_SHORT

#define NIFTI_DT_UNSIGNED_SHORT   512

NIFTI1 data type 16 bits

Definition at line 112 of file tpcnifti.h.

Referenced by imgReadNifti().

NIFTI_INTENT_BETA

#define NIFTI_INTENT_BETA   7

NIFTI1 intent statistics

Definition at line 141 of file tpcnifti.h.

NIFTI_INTENT_BINOM

#define NIFTI_INTENT_BINOM   8

NIFTI1 intent statistics

Definition at line 143 of file tpcnifti.h.

NIFTI_INTENT_CHI

#define NIFTI_INTENT_CHI   19

NIFTI1 intent statistics

Definition at line 165 of file tpcnifti.h.

NIFTI_INTENT_CHISQ

#define NIFTI_INTENT_CHISQ   6

NIFTI1 intent statistics

Definition at line 139 of file tpcnifti.h.

NIFTI_INTENT_CHISQ_NONC

#define NIFTI_INTENT_CHISQ_NONC   13

NIFTI1 intent statistics

Definition at line 153 of file tpcnifti.h.

NIFTI_INTENT_CORREL

#define NIFTI_INTENT_CORREL   2

NIFTI1 intent statistics

Definition at line 131 of file tpcnifti.h.

NIFTI_INTENT_DIMLESS

#define NIFTI_INTENT_DIMLESS   1011

NIFTI1 intent other

Definition at line 197 of file tpcnifti.h.

NIFTI_INTENT_DISPVECT

#define NIFTI_INTENT_DISPVECT   1006

NIFTI1 intent other

Definition at line 187 of file tpcnifti.h.

NIFTI_INTENT_ESTIMATE

#define NIFTI_INTENT_ESTIMATE   1001

NIFTI1 intent other

Definition at line 177 of file tpcnifti.h.

NIFTI_INTENT_EXTVAL

#define NIFTI_INTENT_EXTVAL   21

NIFTI1 intent statistics

Definition at line 169 of file tpcnifti.h.

NIFTI_INTENT_FTEST

#define NIFTI_INTENT_FTEST   4

NIFTI1 intent statistics

Definition at line 135 of file tpcnifti.h.

NIFTI_INTENT_FTEST_NONC

#define NIFTI_INTENT_FTEST_NONC   12

NIFTI1 intent statistics

Definition at line 151 of file tpcnifti.h.

NIFTI_INTENT_GAMMA

#define NIFTI_INTENT_GAMMA   9

NIFTI1 intent statistics

Definition at line 145 of file tpcnifti.h.

NIFTI_INTENT_GENMATRIX

#define NIFTI_INTENT_GENMATRIX   1004

NIFTI1 intent other

Definition at line 183 of file tpcnifti.h.

NIFTI_INTENT_INVGAUSS

#define NIFTI_INTENT_INVGAUSS   20

NIFTI1 intent statistics

Definition at line 167 of file tpcnifti.h.

NIFTI_INTENT_LABEL

#define NIFTI_INTENT_LABEL   1002

NIFTI1 intent other

Definition at line 179 of file tpcnifti.h.

NIFTI_INTENT_LAPLACE

#define NIFTI_INTENT_LAPLACE   15

NIFTI1 intent statistics

Definition at line 157 of file tpcnifti.h.

NIFTI_INTENT_LOG10PVAL

#define NIFTI_INTENT_LOG10PVAL   24

NIFTI1 intent statistics

Definition at line 175 of file tpcnifti.h.

NIFTI_INTENT_LOGISTIC

#define NIFTI_INTENT_LOGISTIC   14

NIFTI1 intent statistics

Definition at line 155 of file tpcnifti.h.

NIFTI_INTENT_LOGPVAL

#define NIFTI_INTENT_LOGPVAL   23

NIFTI1 intent statistics

Definition at line 173 of file tpcnifti.h.

NIFTI_INTENT_NEURONAME

#define NIFTI_INTENT_NEURONAME   1003

NIFTI1 intent other

Definition at line 181 of file tpcnifti.h.

NIFTI_INTENT_NONE

#define NIFTI_INTENT_NONE   0

NIFTI1 intent dataset

Definition at line 129 of file tpcnifti.h.

Referenced by imgSetNiftiHeader().

NIFTI_INTENT_NORMAL

#define NIFTI_INTENT_NORMAL   11

NIFTI1 intent statistics

Definition at line 149 of file tpcnifti.h.

NIFTI_INTENT_POINTSET

#define NIFTI_INTENT_POINTSET   1008

NIFTI1 intent other

Definition at line 191 of file tpcnifti.h.

NIFTI_INTENT_POISSON

#define NIFTI_INTENT_POISSON   10

NIFTI1 intent statistics

Definition at line 147 of file tpcnifti.h.

NIFTI_INTENT_PVAL

#define NIFTI_INTENT_PVAL   22

NIFTI1 intent statistics

Definition at line 171 of file tpcnifti.h.

NIFTI_INTENT_QUATERNION

#define NIFTI_INTENT_QUATERNION   1010

NIFTI1 intent other

Definition at line 195 of file tpcnifti.h.

NIFTI_INTENT_SYMMATRIX

#define NIFTI_INTENT_SYMMATRIX   1005

NIFTI1 intent other

Definition at line 185 of file tpcnifti.h.

NIFTI_INTENT_TRIANGLE

#define NIFTI_INTENT_TRIANGLE   1009

NIFTI1 intent other

Definition at line 193 of file tpcnifti.h.

NIFTI_INTENT_TTEST

#define NIFTI_INTENT_TTEST   3

NIFTI1 intent statistics

Definition at line 133 of file tpcnifti.h.

NIFTI_INTENT_TTEST_NONC

#define NIFTI_INTENT_TTEST_NONC   17

NIFTI1 intent statistics

Definition at line 161 of file tpcnifti.h.

NIFTI_INTENT_UNIFORM

#define NIFTI_INTENT_UNIFORM   16

NIFTI1 intent statistics

Definition at line 159 of file tpcnifti.h.

NIFTI_INTENT_VECTOR

#define NIFTI_INTENT_VECTOR   1007

NIFTI1 intent other

Definition at line 189 of file tpcnifti.h.

NIFTI_INTENT_WEIBULL

#define NIFTI_INTENT_WEIBULL   18

NIFTI1 intent statistics

Definition at line 163 of file tpcnifti.h.

NIFTI_INTENT_ZSCORE

#define NIFTI_INTENT_ZSCORE   5

NIFTI1 intent statistics

Definition at line 137 of file tpcnifti.h.

NIFTI_UNITS_HERTZ

#define NIFTI_UNITS_HERTZ   32

NIFTI1 units: Hertz

Definition at line 58 of file tpcnifti.h.

NIFTI_UNITS_METER

#define NIFTI_UNITS_METER   1

NIFTI1 units: meter

Definition at line 46 of file tpcnifti.h.

Referenced by imgGetNiftiHeader().

NIFTI_UNITS_MICRON

#define NIFTI_UNITS_MICRON   4

NIFTI1 units: micrometer

Definition at line 50 of file tpcnifti.h.

Referenced by imgGetNiftiHeader().

NIFTI_UNITS_MM

#define NIFTI_UNITS_MM   2

NIFTI1 units: millimetre

Definition at line 48 of file tpcnifti.h.

Referenced by imgGetNiftiHeader(), and imgSetNiftiHeader().

NIFTI_UNITS_MSEC

#define NIFTI_UNITS_MSEC   16

NIFTI1 units: milliseconds

Definition at line 54 of file tpcnifti.h.

NIFTI_UNITS_PPM

#define NIFTI_UNITS_PPM   40

NIFTI1 units: parts per million

Definition at line 60 of file tpcnifti.h.

NIFTI_UNITS_RADS

#define NIFTI_UNITS_RADS   48

NIFTI1 units: radians per second

Definition at line 62 of file tpcnifti.h.

NIFTI_UNITS_SEC

#define NIFTI_UNITS_SEC   8

NIFTI1 units: seconds

Definition at line 52 of file tpcnifti.h.

Referenced by imgSetNiftiHeader().

NIFTI_UNITS_UNKNOWN

#define NIFTI_UNITS_UNKNOWN   0

NIFTI1 units: unknown

Definition at line 44 of file tpcnifti.h.

NIFTI_UNITS_USEC

#define NIFTI_UNITS_USEC   24

NIFTI1 units: microseconds

Definition at line 56 of file tpcnifti.h.

NIFTI_XFORM_ALIGNED_ANAT

#define NIFTI_XFORM_ALIGNED_ANAT   2

NIFTI1 Coordinate System: Coordinates aligned to another file or "truth".

Definition at line 204 of file tpcnifti.h.

NIFTI_XFORM_MNI_152

#define NIFTI_XFORM_MNI_152   4

NIFTI1 Coordinate System: Coordinates aligned to the MNI 152 space.

Definition at line 208 of file tpcnifti.h.

NIFTI_XFORM_SCANNER_ANAT

#define NIFTI_XFORM_SCANNER_ANAT   1

NIFTI1 Coordinate System: Scanner-based anatomical coordinates.

Definition at line 202 of file tpcnifti.h.

NIFTI_XFORM_TALAIRACH

#define NIFTI_XFORM_TALAIRACH   3

NIFTI1 Coordinate System: Coordinates aligned to the Talairach-Tournoux atlas.

Definition at line 206 of file tpcnifti.h.

NIFTI_XFORM_UNKNOWN

#define NIFTI_XFORM_UNKNOWN   0

NIFTI1 Coordinate System: Arbitrary coordinates.

Definition at line 200 of file tpcnifti.h.

Function Documentation

anaExists()

int anaExists ( const char * filename, char * hdrfile, char * imgfile, char * siffile, ANALYZE_DSR * header, TPCSTATUS * status )

extern

Verify if specified file name is an Analyze 7.5 file.

Todo

Add tests.

See also

anaReadHeader, niftiExists, micropetExists

Returns

Returns 1 if it is Analyze, 0 if not.

Parameters

filename	File name, either header file, image file, or base name without extensions.
hdrfile	If file name refers to an Analyze file, then header file name will be written in this char pointer (space needs to allocated by caller); If header and image are combined, then this will be the name of combined file; enter NULL if not needed.
imgfile	If file name refers to an Analyze file, then image file name will be written in this char pointer (space needs to allocated by caller); If header and image are combined, then this will be the name of combined file; enter NULL if not needed.
siffile	If file name refers to an Analyze file, and if SIF exists, then SIF file name will be written in this char pointer (space needs to allocated by caller); enter NULL if not needed.
header	Pointer to Analyze header, which is filled in this function; enter NULL, if not needed.
status	Pointer to status data; enter NULL if not needed.

Definition at line 16 of file analyzeio.c.

  {
  int verbose=0; if(status!=NULL) verbose=status->verbose;
  if(verbose>0) {printf("%s(%s, ...)\n", __func__, filename); fflush(stdout);}
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
 
  /* Initiate output */
  if(hdrfile!=NULL) hdrfile[0]=(char)0;
  if(imgfile!=NULL) imgfile[0]=(char)0;
  if(siffile!=NULL) siffile[0]=(char)0;
 
  /* Empty file name means not Analyze file */
  if(strnlen(filename, 2)<1) {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FILENAME);
    return(0);
  }
 
  /* Construct the base file name wo extensions */
  char basefile[FILENAME_MAX]; strlcpy(basefile, filename, FILENAME_MAX); 
  // If file exists it has extensions (similar than NIfTI-1)
  if(fileExist(basefile)) niftiBasename(basefile);
  if(verbose>1) printf("  basefile := %s\n", basefile);
 
  /* Combined header and image file exists? */
  int combined=0;
  char temp[FILENAME_MAX+10], localhdrfile[FILENAME_MAX];
  localhdrfile[0]=(char)0;
  strcpy(temp, basefile); strcat(temp, ".nii");
  if(fileExist(temp)) {
    if(verbose>1) printf("  %s exists.\n", temp);
    /* Preserve header and image file names */
    strcpy(localhdrfile, temp);
    if(hdrfile!=NULL) strlcpy(hdrfile, temp, FILENAME_MAX);
    if(imgfile!=NULL) strlcpy(imgfile, temp, FILENAME_MAX);
    combined=1;
  } else {
    if(verbose>1) printf("  %s does not exist.\n", temp);
    /* Not combined file, therefore check that header file exists */
    strcpy(temp, basefile); strcat(temp, ".hdr");
    if(!fileExist(temp)) {
      strcpy(temp, basefile); strcat(temp, ".img.hdr");
      if(!fileExist(temp)) {
        if(verbose>1) printf("  hdr file not found.\n");
        statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_MISSING_HEADER);
        return(0);
      }
    }
    /* Preserve file name of the header */
    strlcpy(localhdrfile, temp, FILENAME_MAX);
    if(hdrfile!=NULL) strlcpy(hdrfile, temp, FILENAME_MAX);
    if(verbose>1) printf("  %s is found.\n", localhdrfile);
    /* Not combined file, therefore check that image file exists */
    strcpy(temp, basefile); strcat(temp, ".img");
    if(!fileExist(temp)) {
      if(verbose>1) printf("  %s not found.\n", temp);
      statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_FILE);
      return(0);
    }
    /* Preserve image filename */
    if(imgfile!=NULL) strlcpy(imgfile, temp, FILENAME_MAX);
    if(verbose>1) printf("  %s is found.\n", temp);
  }
  if(verbose>1) {printf("  combined := %d\n", combined); fflush(stdout);}
 
  /* Read header to check that this indeed is Analyze */
  {
    ANALYZE_DSR *dsr, local_dsr; if(header==NULL) dsr=&local_dsr; else dsr=header;
    int ret=anaReadHeader(localhdrfile, dsr, verbose-2);
    if(ret!=TPCERROR_OK) {
      if(verbose>1) {
        printf("  %s was not identified as Analyze header file.\n", localhdrfile); fflush(stdout);}
      statusSet(status, __func__, __FILE__, __LINE__, ret);
      return(0);
    }
    if(verbose>1) {printf("  %s is identified as Analyze.\n", localhdrfile); fflush(stdout);}
  }
 
  /* SIF exists? */
  strcpy(temp, basefile); strcat(temp, ".sif");
  if(verbose>3) printf("  checking if %s exists\n", temp);
  if(!fileExist(temp)) {
    strcpy(temp, basefile); strcat(temp, ".img.sif");
    if(verbose>3) printf("  checking if %s exists\n", temp);
    if(!fileExist(temp)) {
      strcpy(temp, basefile); strcat(temp, ".nii.sif");
      if(verbose>3) printf("  checking if %s exists\n", temp);
      if(!fileExist(temp)) {
        if(verbose>0) printf("  SIF not found or accessible.\n");
        statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
        return(1); // but otherwise ok NIfTI
      }
    }
  }
  /* Preserve SIF filename */
  if(siffile!=NULL) strcpy(siffile, temp);
  if(verbose>1) {printf("  %s is found.\n", temp); fflush(stdout);}
 
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
  return(1);
}

Referenced by imgRead().

anaReadHeader()

int anaReadHeader ( const char * filename, ANALYZE_DSR * dsr, int verbose )

extern

Read Analyze header contents.

Todo

Add tests.

See also

anaExists, micropetHeaderRead

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

filename	Name of file to read (including path and extension).
dsr	Pointer to previously allocated header structure.
verbose	Verbose level; if zero, then nothing is printed to stderr or stdout

Definition at line 144 of file analyzeio.c.

  {
  if(verbose>0) {printf("%s(%s, ...)\n", __func__, filename); fflush(stdout);}
 
  /* Check arguments */
  if(strnlen(filename, 2)<1) return(TPCERROR_INVALID_FILENAME);
  if(dsr==NULL) return(TPCERROR_FAIL);
 
  /* Is current platform little endian (1) or not (0) ? */
  int little=endianLittle();
  if(verbose>2) {
    if(little) printf("little endian platform\n"); else printf("big endian platform\n");
  }
 
  /* Open file */
  FILE *fp=fopen(filename, "rb"); if(fp==NULL) return(TPCERROR_CANNOT_OPEN);
 
  /* Try to read the size of header, which should be stored in the beginning as
     4-byte integer in both NIfTI and Analyze header files. */
  int same_order=1;
  int hdrSize=0;
  {
    char buf[4];
    if(fread(buf, 4, 1, fp)<1) {fclose(fp); return(TPCERROR_CANNOT_READ);}
    memcpy(&hdrSize, buf, 4); 
    if(hdrSize!=ANALYZE_HEADER_SIZE && hdrSize!=NIFTI2_HEADER_SIZE) {
      swawbip(&hdrSize, 4); same_order=0;
    }
    if(verbose>1) {printf("  sizeof_hdr := %d\n", hdrSize); fflush(stdout);}
    if(hdrSize==NIFTI2_HEADER_SIZE) {
      if(verbose>1) {printf("  NIfTI-2 header size.\n"); fflush(stdout);}
      fclose(fp); return(TPCERROR_INVALID_FORMAT);
    } else if(hdrSize==ANALYZE_HEADER_SIZE) {
      if(verbose>1) {printf("  Analyze or NIfTI-1 header size.\n"); fflush(stdout);}
    } else {
      if(verbose>1) {printf("  invalid Analyze sizeof_hdr\n"); fflush(stdout);}
      return(TPCERROR_INVALID_FORMAT);
    }
  }
 
 
  /* Read file into Analyze header structure */
  if(verbose>1) {printf("  reading header as binary data\n"); fflush(stdout);}
  unsigned char buf[ANALYZE_HEADER_SIZE];
  if(fread(buf, ANALYZE_HEADER_SIZE, 1, fp)<1) {fclose(fp); return(TPCERROR_CANNOT_READ);}
  /* Close file */
  fclose(fp);
 
  /* Check that header does not have the Nifti Magic number */
  char magic[4]; 
  memcpy(magic, buf+344, 4); magic[3]=(char)0;
  if(strcasecmp(magic, "ni1")==0 || strcasecmp(magic, "n+1")==0) {
    if(verbose>1) {printf("  Nifti magic number was found"); fflush(stdout);}
    return(TPCERROR_INVALID_FORMAT);
  }
 
  /* Set the original byte order */
  if(same_order) dsr->byte_order=little;
  else {if(little==1) dsr->byte_order=0; else dsr->byte_order=1;}
 
  /* Set key header structure contents */
  dsr->h.sizeof_hdr=hdrSize;
  memcpy(dsr->h.data_type, buf+4, 10);
  memcpy(dsr->h.db_name, buf+14, 18);
  if(!same_order) swawbip(buf+32, 4);
  memcpy(&dsr->h.extents, buf+32, 4);
  if(!same_order) swabip(buf+36, 2);
  memcpy(&dsr->h.session_error, buf+36, 2);
  memcpy(&dsr->h.regular, buf+38, 1);
  memcpy(&dsr->h.hkey_un0, buf+39, 1);
 
  /* Set image dimension header structure contents */
  if(!same_order) swabip(buf+40, 16);
  memcpy(dsr->h.dim, buf+40, 16);
  if(!same_order) swabip(buf+56, 2);
  memcpy(&dsr->h.unused8, buf+56, 2);
  if(!same_order) swabip(buf+58, 2);
  memcpy(&dsr->h.unused9, buf+58, 2);
  if(!same_order) swabip(buf+60, 2);
  memcpy(&dsr->h.unused10, buf+60, 2);
  if(!same_order) swabip(buf+62, 2);
  memcpy(&dsr->h.unused11, buf+62, 2);
  if(!same_order) swabip(buf+64, 2);
  memcpy(&dsr->h.unused12, buf+64, 2);
  if(!same_order) swabip(buf+66, 2);
  memcpy(&dsr->h.unused13, buf+66, 2);
  if(!same_order) swabip(buf+68, 2);
  memcpy(&dsr->h.unused14, buf+68, 2);
  if(!same_order) swabip(buf+70, 2);
  memcpy(&dsr->h.datatype, buf+70, 2);
  if(!same_order) swabip(buf+72, 2);
  memcpy(&dsr->h.bitpix, buf+72, 2);
  if(!same_order) swabip(buf+74, 2);
  memcpy(&dsr->h.dim_un0, buf+74, 2);
  if(!same_order) swawbip(buf+76, 32);
  memcpy(dsr->h.pixdim, buf+76, 32);
  if(!same_order) swawbip(buf+108, 4);
  memcpy(&dsr->h.vox_offset, buf+108, 4);
  if(!same_order) swawbip(buf+112, 4);
  memcpy(&dsr->h.funused1, buf+112, 4);
  if(!same_order) swawbip(buf+116, 4);
  memcpy(&dsr->h.funused2, buf+116, 4);
  if(!same_order) swawbip(buf+120, 4);
  memcpy(&dsr->h.funused3, buf+120, 4);
  if(!same_order) swawbip(buf+124, 4);
  memcpy(&dsr->h.cal_max, buf+124, 4);
  if(!same_order) swawbip(buf+128, 4);
  memcpy(&dsr->h.cal_min, buf+128, 4);
  if(!same_order) swawbip(buf+132, 4);
  memcpy(&dsr->h.compressed, buf+132, 4);
  if(!same_order) swawbip(buf+136, 4);
  memcpy(&dsr->h.verified, buf+136, 4);
  if(!same_order) swawbip(buf+140, 4);
  memcpy(&dsr->h.glmax, buf+140, 4);
  if(!same_order) swawbip(buf+144, 4);
  memcpy(&dsr->h.glmin, buf+144, 4);
 
  /* Set data history header structure contents */
  memcpy(dsr->h.descrip, buf+148, 80);
  memcpy(dsr->h.aux_file, buf+228, 24);
  memcpy(&dsr->h.orient, buf+252, 1);
  memcpy(dsr->h.originator, buf+253, 10);
  memcpy(dsr->h.generated, buf+263, 10);
  memcpy(dsr->h.scannum, buf+273, 10);
  memcpy(dsr->h.patient_id, buf+283, 10);
  memcpy(dsr->h.exp_date, buf+293, 10);
  memcpy(dsr->h.exp_time, buf+303, 10);
  memcpy(dsr->h.hist_un0, buf+313, 3);
  if(!same_order) swawbip(buf+316, 4);
  memcpy(&dsr->h.views, buf+316, 4);
  if(!same_order) swawbip(buf+320, 4);
  memcpy(&dsr->h.vols_added, buf+320, 4);
  if(!same_order) swawbip(buf+324, 4);
  memcpy(&dsr->h.start_field, buf+324,4);
  if(!same_order) swawbip(buf+328, 4);
  memcpy(&dsr->h.field_skip, buf+328, 4);
  if(!same_order) swawbip(buf+332, 4);
  memcpy(&dsr->h.omax, buf+332, 4);
  if(!same_order) swawbip(buf+336, 4);
  memcpy(&dsr->h.omin, buf+336, 4);
  if(!same_order) swawbip(buf+340, 4);
  memcpy(&dsr->h.smax, buf+340, 4);
  if(!same_order) swawbip(buf+344, 4);
  memcpy(&dsr->h.smin, buf+344, 4);
 
  /* Check header contents */
  if(dsr->h.extents!=16384 && dsr->h.extents!=0) {
    if(verbose>0) printf("h.extents := %d\n", dsr->h.extents);
    return(TPCERROR_UNSUPPORTED);
  }
  if(dsr->h.regular!='r') {
    if(verbose>1) printf("h.regular := %c\n", dsr->h.regular);
    return(TPCERROR_UNSUPPORTED);
  }
 
  if(verbose>1) {printf("  complete Analyze header was read.\n"); fflush(stdout);}
 
  return(TPCERROR_OK);
}

Referenced by anaExists().

niftiBasename()

void niftiBasename ( char * filename )

extern

Remove any extensions from NIfTI file name, leaving only base file name. Possible path is kept.

Parameters

filename

Full name of file.

Definition at line 14 of file niftiname.c.

  {
  if(filename==NULL) return;
  char basename[FILENAME_MAX];
  strncpyCleanSpaces(basename, filename, FILENAME_MAX);
  strcpy(filename, "");
  char *cptr=filenameGetExtension(basename);
  if(cptr!=NULL) {
    if(strcasecmp(cptr, ".hdr")==0) *cptr=(char)0;
    else if(strcasecmp(cptr, ".nii")==0) *cptr=(char)0;
    else if(strcasecmp(cptr, ".img")==0) *cptr=(char)0;
    else if(strcasecmp(cptr, ".sif")==0) *cptr=(char)0;
    else if(strcasecmp(cptr, ".")==0) *cptr=(char)0;
  }
  /* Remove also double extensions, e.g. from data.img.hdr */
  cptr=filenameGetExtension(basename);
  if(cptr!=NULL) {
    if(strcasecmp(cptr, ".nii")==0) *cptr=(char)0;
    else if(strcasecmp(cptr, ".img")==0) *cptr=(char)0;
    else if(strcasecmp(cptr, ".")==0) *cptr=(char)0;
  }
  strcpy(filename, basename);
  return;
}

Referenced by anaExists(), imgWriteNifti(), niftiCreateFNames(), and niftiExists().

niftiExists()

int niftiExists ( const char * filename, char * hdrfile, char * imgfile, char * siffile, NIFTI_DSR * header, TPCSTATUS * status )

extern

Verify if specified file name is a NIfTI file.

Todo

Add tests.

See also

niftiReadHeader, anaExists, micropetExists

Returns

Returns 1 if it is NIfTI, and 0 if it is not NIfTI. Error code set in TPCSTATUS.

Parameters

filename	File name, either header file, image file, or base name without extensions.
hdrfile	If file name refers to a NIfTI file, then header file name will be written in this char pointer (space needs to allocated by caller); If header and image are combined, then this will be the name of combined file; enter NULL if not needed.
imgfile	If file name refers to a NIfTI file, then image file name will be written in this char pointer (space needs to allocated by caller); If header and image are combined, then this will be the name of combined file; enter NULL if not needed.
siffile	If file name refers to a NIfTI file, and if SIF exists, then SIF file name will be written in this char pointer (space needs to allocated by caller); enter NULL if not needed.
header	Pointer to NIfTI header, which is filled in this function; enter NULL, if not needed.
status	Pointer to status data; enter NULL if not needed.

Definition at line 17 of file niftiio.c.

  {
  int verbose=0; if(status!=NULL) verbose=status->verbose;
  if(verbose>0) {printf("%s(%s, ...)\n", __func__, filename); fflush(stdout);}
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
 
  /* Initiate output */
  if(hdrfile!=NULL) hdrfile[0]=(char)0;
  if(imgfile!=NULL) imgfile[0]=(char)0;
  if(siffile!=NULL) siffile[0]=(char)0;
 
  /* Empty file name means not a NIfTI */
  if(strnlen(filename, 2)<1) {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FILENAME);
    return(0);
  }
 
  /* Construct the base file name wo extensions */
  char basefile[FILENAME_MAX]; strlcpy(basefile, filename, FILENAME_MAX); 
  // If file exists it has extensions
  if(fileExist(basefile)) niftiBasename(basefile);
  if(verbose>1) printf("  basefile := %s\n", basefile);
 
  /* Combined header and image file exists? */
  int combined=0;
  char temp[FILENAME_MAX+10], localhdrfile[FILENAME_MAX];
  localhdrfile[0]=(char)0;
  strcpy(temp, basefile); strcat(temp, ".nii");
  if(fileExist(temp)) {
    if(verbose>1) printf("  %s exists.\n", temp);
    /* Preserve header and image file names */
    strcpy(localhdrfile, temp);
    if(hdrfile!=NULL) strlcpy(hdrfile, temp, FILENAME_MAX);
    if(imgfile!=NULL) strlcpy(imgfile, temp, FILENAME_MAX);
    combined=1;
  } else {
    if(verbose>1) printf("  %s does not exist.\n", temp);
    /* Not combined file, therefore check that header file exists */
    strcpy(temp, basefile); strcat(temp, ".hdr");
    if(!fileExist(temp)) {
      strcpy(temp, basefile); strcat(temp, ".img.hdr");
      if(!fileExist(temp)) {
        if(verbose>1) printf("  hdr file not found.\n");
        statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_MISSING_HEADER);
        return(0);
      }
    }
    /* Preserve file name of the header */
    strlcpy(localhdrfile, temp, FILENAME_MAX);
    if(hdrfile!=NULL) strlcpy(hdrfile, temp, FILENAME_MAX);
    if(verbose>1) printf("  %s is found.\n", localhdrfile);
    /* Not combined file, therefore check that image file exists */
    strcpy(temp, basefile); strcat(temp, ".img");
    if(!fileExist(temp)) {
      if(verbose>1) printf("  %s not found.\n", temp);
      statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_FILE);
      return(0);
    }
    /* Preserve image filename */
    if(imgfile!=NULL) strlcpy(imgfile, temp, FILENAME_MAX);
    if(verbose>1) printf("  %s is found.\n", temp);
  }
  if(verbose>1) {printf("  combined := %d\n", combined); fflush(stdout);}
 
  /* Read header to check that this indeed is NIfTI, and which version of it */
  {
    NIFTI_DSR *dsr, local_dsr; if(header==NULL) dsr=&local_dsr; else dsr=header;
    int ret=niftiReadHeader(localhdrfile, dsr, verbose-2);
    if(ret!=TPCERROR_OK) {
      if(verbose>1) {
        printf("  %s was not identified as NIfTI header file.\n", localhdrfile); fflush(stdout);}
      statusSet(status, __func__, __FILE__, __LINE__, ret);
      return(0);
    }
    if(verbose>1) {printf("  %s is identified as NIfTI.\n", localhdrfile); fflush(stdout);}
  }
 
  /* SIF exists? */
  strcpy(temp, basefile); strcat(temp, ".sif");
  if(verbose>3) printf("  checking if %s exists\n", temp);
  if(!fileExist(temp)) {
    strcpy(temp, basefile); strcat(temp, ".img.sif");
    if(verbose>3) printf("  checking if %s exists\n", temp);
    if(!fileExist(temp)) {
      strcpy(temp, basefile); strcat(temp, ".nii.sif");
      if(verbose>3) printf("  checking if %s exists\n", temp);
      if(!fileExist(temp)) {
        if(verbose>0) printf("  SIF not found or accessible.\n");
        statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
        return(1); // but otherwise ok NIfTI
      }
    }
  }
  /* Preserve SIF filename */
  if(siffile!=NULL) strcpy(siffile, temp);
  if(verbose>1) {printf("  %s is found.\n", temp); fflush(stdout);}
 
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
  return(1);
}

Referenced by imgRead(), and imgReadNifti().

niftiReadHeader()

int niftiReadHeader ( const char * filename, NIFTI_DSR * dsr, int verbose )

extern

Read NIfTI-1 header contents, including 4-byte extender.

Remarks

Currently does not read NIfTI header extension.

Todo

Add tests.

See also

niftiWriteHeader, niftiExists, anaReadHeader, micropetHeaderRead

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

filename	Name of file to read (including path and extension).
dsr	Pointer to previously allocated header structure.
verbose	Verbose level; if zero, then nothing is printed to stderr or stdout.

Definition at line 146 of file niftiio.c.

  {
  if(verbose>0) {printf("%s(%s, ...)\n", __func__, filename); fflush(stdout);}
 
  /* Check arguments */
  if(strnlen(filename, 2)<1) return(TPCERROR_INVALID_FILENAME);
  if(dsr==NULL) return(TPCERROR_FAIL);
 
  /* Is current platform little endian (1) or not (0) ? */
  int little=endianLittle();
  if(verbose>2) {
    if(little) printf("little endian platform\n"); else printf("big endian platform\n");
  }
 
  /* Open file */
  FILE *fp=fopen(filename, "rb"); if(fp==NULL) return(TPCERROR_CANNOT_OPEN);
 
  /* Try to read the size of header, which should be stored in the beginning as
     4-byte integer in both NIfTI and Analyze header files.
     Determine from the size if byte swapping is needed. */
  int hdrSize=0;
  int same_order=1;
  {
    char buf[4];
    if(fread(buf, 4, 1, fp)<1) {fclose(fp); return(TPCERROR_CANNOT_READ);}
    memcpy(&hdrSize, buf, 4); 
    if(hdrSize!=NIFTI1_HEADER_SIZE && hdrSize!=NIFTI2_HEADER_SIZE) {
      swawbip(&hdrSize, 4);
      same_order=0;
    }
    if(verbose>1) {printf("  sizeof_hdr := %d\n", hdrSize); fflush(stdout);}
    if(hdrSize==NIFTI2_HEADER_SIZE) {
      if(verbose>1) {printf("  NIfTI-2 header size.\n"); fflush(stdout);}
    } else if(hdrSize==NIFTI1_HEADER_SIZE) {
      if(verbose>1) {printf("  NIfTI-1 or Analyze header size.\n"); fflush(stdout);}
    } else {
      if(verbose>1) {printf("  invalid Nifti sizeof_hdr\n"); fflush(stdout);}
      fclose(fp); return(TPCERROR_INVALID_FORMAT);
    }
  }
  if(same_order==1) {
    dsr->byte_order=little;
  } else {
    // opposite order in file and in current machine
    if(little==1) dsr->byte_order=0; else dsr->byte_order=1;
  }
  if(verbose>1) {
    printf("  Nifti byte order := ");
    if(dsr->byte_order==0) printf("big\n"); else printf("little\n");
    if(same_order==1) printf("  No need for byte swapping\n");
    else printf("  Byte swapping needed.\n");
    fflush(stdout);
  }
 
 
  /* Read file into NIfTI header structure */
  if(verbose>1) {printf("  reading header as binary data\n"); fflush(stdout);}
  unsigned char buf[hdrSize];
  rewind(fp);
  if(fread(buf, hdrSize, 1, fp)<1) {fclose(fp); return(TPCERROR_CANNOT_READ);}
 
  /* Read NIfTI-1 extender */
  int extender=0;
  for(int n=0; n<4; n++) dsr->e.extension[n]=(char)0;
  if(fread(dsr->e.extension, 4, 1, fp)<1) {
    if(verbose>1) printf("  Nifti header extender not found in %s\n", filename);
    extender=0;
  } else {
    if(verbose>2) printf("  Nifti header extender was found in %s\n", filename);
    extender=1;
  }
  /* Close file */
  fclose(fp);
 
  /* Get the Nifti Magic number */
  if(hdrSize==NIFTI1_HEADER_SIZE) {
    if(buf[344]==(char)0 || buf[344]=='0') {
      if(verbose>0) {printf("  probably Analyze header.\n"); fflush(stdout);}
      return(TPCERROR_UNSUPPORTED);
    }
    memcpy(dsr->h1.magic, buf+344, 4);
    dsr->h1.magic[3]=(char)0; // make sure that string ends as intended
    if(strcasecmp(dsr->h1.magic, "ni1")==0) {
      if(verbose>1) {printf("  separate hdr and img files.\n"); fflush(stdout);}
    } else if(strcasecmp(dsr->h1.magic, "n+1")==0) {
      if(verbose>1) {printf("  combined hdr and img data.\n"); fflush(stdout);}
    } else {
      if(verbose>1) {printf("  Nifti magic number not found"); fflush(stdout);}
      if(verbose>2) {
        printf("magic := {%d, %d, %d, %d}\n", dsr->h1.magic[0], dsr->h1.magic[1],
                dsr->h1.magic[2], dsr->h1.magic[3]);
      } 
      return(TPCERROR_INVALID_FORMAT);
    }
    dsr->n=1;
    if(verbose>1) printf("  Nifti Magic number := %s\n", dsr->h1.magic);
    /* Check that 4-byte header extender was found, if magic number is n+1 */
    if(strcasecmp(dsr->h1.magic, "n+1")==0 && extender==0) {
      if(verbose>1) printf("  Nifti n+1 header extender not found\n");
      return(TPCERROR_INVALID_FORMAT);
    }
  } else {
    memcpy(dsr->h2.magic, buf+4, 8);
    if(strcasecmp(dsr->h2.magic, "ni2")==0) {
      if(verbose>1) {printf("  separate hdr and img files.\n"); fflush(stdout);}
    } else if(strcasecmp(dsr->h2.magic, "n+2")==0) {
      if(verbose>1) {printf("  combined hdr and img data.\n"); fflush(stdout);}
    } else {
      if(verbose>1) {printf("  Nifti magic number not found"); fflush(stdout);}
      return(TPCERROR_INVALID_FORMAT);
    }
    /* Check also the next four characters of NIfTI-2 signature */
    if(dsr->h2.magic[4]!='\r' || dsr->h2.magic[5]!='\n' || dsr->h2.magic[6]!=32 || dsr->h2.magic[7]!='\n') {
      if(verbose>1) {printf("  Nifti magic signature not found"); fflush(stdout);}
      return(TPCERROR_INVALID_FORMAT);
    }
    dsr->n=2;
    if(verbose>1) printf("  Nifti Magic number := %s\n", dsr->h2.magic);
    /* Check that 4-byte header extender was found, if magic number is n+1 */
    if(strcasecmp(dsr->h2.magic, "n+3")==0 && extender==0) {
      if(verbose>1) printf("  Nifti n+3 header extender not found\n");
      return(TPCERROR_INVALID_FORMAT);
    }
  }
 
 
  /*
   *  Fill the header structure fields
   */
  if(dsr->n==1) { // NIfTI-1
    dsr->h1.sizeof_hdr=hdrSize; // Bytes already swapped when necessary
    memcpy(&dsr->h1.data_type, buf+4, 10);
    memcpy(&dsr->h1.db_name, buf+14, 18);
    if(!same_order) swawbip(buf+32, 4);
    memcpy(&dsr->h1.extents, buf+32, 4);
    if(!same_order) swabip(buf+36, 2);
    memcpy(&dsr->h1.session_error, buf+36, 2);
    memcpy(&dsr->h1.regular, buf+38, 1);
    memcpy(&dsr->h1.dim_info, buf+39, 1);
 
    /* dim */
    if(!same_order) swabip(buf+40, 16);
    memcpy(dsr->h1.dim, buf+40, 16);
    /* intent parameters */
    if(!same_order) swawbip(buf+56, 4);
    memcpy(&dsr->h1.intent_p1, buf+56, 4);
    if(!same_order) swawbip(buf+60, 4);
    memcpy(&dsr->h1.intent_p2, buf+60, 4);
    if(!same_order) swawbip(buf+64, 4);
    memcpy(&dsr->h1.intent_p3, buf+64, 4);
    if(!same_order) swabip(buf+68, 2);
    memcpy(&dsr->h1.intent_code, buf+68, 2);
 
    /*  */
    if(!same_order) swabip(buf+70, 2);
    memcpy(&dsr->h1.datatype, buf+70, 2);
    if(!same_order) swabip(buf+72, 2);
    memcpy(&dsr->h1.bitpix, buf+72, 2);
    if(!same_order) swabip(buf+74, 2);
    memcpy(&dsr->h1.slice_start, buf+74, 2);
    if(!same_order) swawbip(buf+76, 32);
    memcpy(dsr->h1.pixdim, buf+76, 32);
    if(!same_order) swawbip(buf+108, 4);
    memcpy(&dsr->h1.vox_offset, buf+108, 4); //printf("dsr->h1.vox_offset := %g\n", dsr->h1.vox_offset);
    if(!same_order) swawbip(buf+112, 4);
    memcpy(&dsr->h1.scl_slope, buf+112, 4);
    if(!same_order) swawbip(buf+116, 4);
    memcpy(&dsr->h1.scl_inter, buf+116, 4);
    if(!same_order) swabip(buf+120, 2);
    memcpy(&dsr->h1.slice_end, buf+120, 2);
    memcpy(&dsr->h1.slice_code, buf+122, 1);
    memcpy(&dsr->h1.xyzt_units, buf+123, 1);
    if(!same_order) swawbip(buf+124, 4);
    memcpy(&dsr->h1.cal_max, buf+124, 4);
    if(!same_order) swawbip(buf+128, 4);
    memcpy(&dsr->h1.cal_min, buf+128, 4);
    if(!same_order) swawbip(buf+132, 4);
    memcpy(&dsr->h1.slice_duration,buf+132,4);
    if(!same_order) swawbip(buf+136, 4);
    memcpy(&dsr->h1.toffset, buf+136, 4);
    if(!same_order) swawbip(buf+140, 4);
    memcpy(&dsr->h1.glmax, buf+140, 4);
    if(!same_order) swawbip(buf+144, 4);
    memcpy(&dsr->h1.glmin, buf+144, 4);
 
    /* study description */
    memcpy(&dsr->h1.descrip, buf+148, 80);
    /* Auxiliary filename */
    memcpy(&dsr->h1.aux_file, buf+228, 24);
 
    /* Transformation parameters */
    if(!same_order) swabip(buf+252, 2);
    memcpy(&dsr->h1.qform_code, buf+252, 2);
    if(!same_order) swabip(buf+254, 2);
    memcpy(&dsr->h1.sform_code, buf+254, 2);
    if(!same_order) swawbip(buf+256, 4);
    memcpy(&dsr->h1.quatern_b, buf+256, 4);
    if(!same_order) swawbip(buf+260, 4);
    memcpy(&dsr->h1.quatern_c, buf+260, 4);
    if(!same_order) swawbip(buf+264, 4);
    memcpy(&dsr->h1.quatern_d, buf+264, 4);
    if(!same_order) swawbip(buf+268, 4);
    memcpy(&dsr->h1.qoffset_x, buf+268, 4);
    if(!same_order) swawbip(buf+272, 4);
    memcpy(&dsr->h1.qoffset_y, buf+272, 4);
    if(!same_order) swawbip(buf+276, 4);
    memcpy(&dsr->h1.qoffset_z, buf+276, 4);
    if(!same_order) swawbip(buf+280, 16);
    memcpy(dsr->h1.srow_x, buf+280, 16);
    if(!same_order) swawbip(buf+296, 16);
    memcpy(dsr->h1.srow_y, buf+296, 16);
    if(!same_order) swawbip(buf+312, 16);
    memcpy(dsr->h1.srow_z, buf+312, 16);
 
    memcpy(&dsr->h1.intent_name, buf+328, 16);
 
  } else { // NIfTI-2
 
    dsr->h2.sizeof_hdr=hdrSize; // Bytes already swapped when necessary
    // magic signature already set
    if(!same_order) swap16ip(buf+12, 1);
    memcpy(&dsr->h2.datatype, buf+12, 2);
    if(!same_order) swap16ip(buf+14, 1);
    memcpy(&dsr->h2.bitpix, buf+14, 2);
    if(!same_order) swap64ip(buf+16, 8);
    memcpy(dsr->h2.dim, buf+16, 64);
    if(!same_order) swap64ip(buf+80, 3); /* intent parameters */
    memcpy(&dsr->h2.intent_p1, buf+80, 8);
    memcpy(&dsr->h2.intent_p2, buf+88, 8);
    memcpy(&dsr->h2.intent_p3, buf+96, 8);
    if(!same_order) swap64ip(buf+104, 8); /* pixdim array */
    memcpy(dsr->h2.pixdim, buf+104, 64);
    if(!same_order) swap64ip(buf+168, 1);
    memcpy(&dsr->h2.vox_offset, buf+168, 8);
    if(!same_order) swap64ip(buf+176, 6);
    memcpy(&dsr->h2.scl_slope, buf+176, 8);
    memcpy(&dsr->h2.scl_inter, buf+184, 8);
    memcpy(&dsr->h2.cal_max, buf+192, 8);
    memcpy(&dsr->h2.cal_min, buf+200, 8);
    memcpy(&dsr->h2.slice_duration, buf+208, 8);
    memcpy(&dsr->h2.toffset, buf+216, 8);
    if(!same_order) swap64ip(buf+224, 2);
    memcpy(&dsr->h2.slice_start, buf+224, 8);
    memcpy(&dsr->h2.slice_end, buf+232, 8);
    memcpy(&dsr->h2.descrip, buf+240, 80); /* study description */
    memcpy(&dsr->h2.aux_file, buf+320, 24);
    if(!same_order) swap32ip(buf+344, 2); /* quaternion fields */
    memcpy(&dsr->h2.qform_code, buf+344, 4);
    memcpy(&dsr->h2.sform_code, buf+348, 4);
    if(!same_order) swap64ip(buf+352, 18);
    memcpy(&dsr->h2.quatern_b, buf+252, 8);
    memcpy(&dsr->h2.quatern_c, buf+260, 8);
    memcpy(&dsr->h2.quatern_d, buf+268, 8);
    memcpy(&dsr->h2.qoffset_x, buf+276, 8);
    memcpy(&dsr->h2.qoffset_y, buf+284, 8);
    memcpy(&dsr->h2.qoffset_z, buf+292, 8);
    memcpy(dsr->h2.srow_x, buf+400, 8);
    memcpy(dsr->h2.srow_x+1, buf+408, 8);
    memcpy(dsr->h2.srow_x+2, buf+416, 8);
    memcpy(dsr->h2.srow_x+3, buf+424, 8);
    memcpy(dsr->h2.srow_y, buf+432, 8);
    memcpy(dsr->h2.srow_y+1, buf+440, 8);
    memcpy(dsr->h2.srow_y+2, buf+448, 8);
    memcpy(dsr->h2.srow_y+3, buf+456, 8);
    memcpy(dsr->h2.srow_z, buf+464, 8);
    memcpy(dsr->h2.srow_z+1, buf+472, 8);
    memcpy(dsr->h2.srow_z+2, buf+480, 8);
    memcpy(dsr->h2.srow_z+3, buf+488, 8);
    if(!same_order) swap32ip(buf+496, 1);
    memcpy(&dsr->h2.slice_code, buf+496, 4);
    if(!same_order) swap32ip(buf+500, 1);
    memcpy(&dsr->h2.xyzt_units, buf+500, 4);
    if(!same_order) swap32ip(buf+504, 1); /* intent */
    memcpy(&dsr->h2.intent_code, buf+508, 4);
    memcpy(&dsr->h2.intent_name, buf+508, 16);
    memcpy(&dsr->h2.dim_info, buf+524, 1);
    memcpy(&dsr->h2.unused_str, buf+525, 15);
  }
 
  if(verbose>1) {printf("  complete Nifti header was read.\n"); fflush(stdout);}
  
 
  return(TPCERROR_OK);
}

Referenced by niftiExists().

niftiWriteHeader()

int niftiWriteHeader ( const char * filename, NIFTI_DSR * dsr, int verbose )

extern

Write NIfTI-1 header contents, including 4-byte extender.

Remarks

Currently does not write header extension.

Todo

Add tests.

See also

niftiExists, niftiReadHeader

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

filename	Name of file to read (including path and extension).
dsr	Pointer to header structure to write.
verbose	Verbose level; if zero, then nothing is printed to stderr or stdout.

Definition at line 445 of file niftiio.c.

  {
  if(verbose>0) {printf("%s(%s, dsr, %d)\n", __func__, filename, verbose); fflush(stdout);}
 
  /* Check arguments */
  if(strnlen(filename, 2)<1) return(TPCERROR_INVALID_FILENAME);
  if(dsr==NULL) return(TPCERROR_FAIL);
 
  /* Check magic number */
  if(dsr->n==1) {
    if(strncmp(dsr->h1.magic, "ni1", 3)!=0 && strncmp(dsr->h1.magic, "n+1", 3)!=0)
      return(TPCERROR_INVALID_FORMAT);
  } else if(dsr->n==2) {
    if(strncmp(dsr->h2.magic, "ni2", 3)!=0 && strncmp(dsr->h2.magic, "n+2", 3)!=0)
      return(TPCERROR_INVALID_FORMAT);
  } else
    return(TPCERROR_FAIL);
 
  /* Is current platform little endian (1) or not (0) ? */
  int little=endianLittle();
  if(verbose>2) {
    if(little) printf("little endian platform\n"); else printf("big endian platform\n");
  }
  int same_order=0;
  if(little==dsr->byte_order) same_order=1;
 
 
  /* Set up buffer with contents of all zeroes */
  unsigned int hdrSize=NIFTI1_HEADER_SIZE; if(dsr->n==2) hdrSize=NIFTI2_HEADER_SIZE;
  unsigned char buf[hdrSize];
  memset(buf, 0, sizeof(hdrSize));
 
  /* Copy header contents into the buffer */
  if(verbose>2) printf("  setting write buffer\n");
  if(dsr->n==1) {
    unsigned char *bptr=buf+0; memcpy(bptr, &dsr->h1.sizeof_hdr, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+4; memcpy(bptr, &dsr->h1.data_type, 10);
    bptr=buf+14; memcpy(bptr, &dsr->h1.db_name, 18);
    bptr=buf+32; memcpy(bptr, &dsr->h1.extents, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+36; memcpy(bptr, &dsr->h1.session_error, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+38; memcpy(bptr, &dsr->h1.regular, 1);
    bptr=buf+39; memcpy(bptr, &dsr->h1.dim_info, 1);
 
    bptr=buf+40; memcpy(bptr, dsr->h1.dim, 16); if(!same_order) swabip(bptr, 16);
    bptr=buf+56; memcpy(bptr, &dsr->h1.intent_p1, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+60; memcpy(bptr, &dsr->h1.intent_p2, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+64; memcpy(bptr, &dsr->h1.intent_p3, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+68; memcpy(bptr, &dsr->h1.intent_code, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+70; memcpy(bptr, &dsr->h1.datatype, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+72; memcpy(bptr, &dsr->h1.bitpix, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+74; memcpy(bptr, &dsr->h1.slice_start, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+76; memcpy(bptr, dsr->h1.pixdim, 32); if(!same_order) swawbip(bptr, 32);
    bptr=buf+108; memcpy(bptr, &dsr->h1.vox_offset, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+112; memcpy(bptr, &dsr->h1.scl_slope, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+116; memcpy(bptr, &dsr->h1.scl_inter, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+120; memcpy(bptr, &dsr->h1.slice_end, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+122; memcpy(bptr, &dsr->h1.slice_code, 1);
    bptr=buf+123; memcpy(bptr, &dsr->h1.xyzt_units, 1);
    bptr=buf+124; memcpy(bptr, &dsr->h1.cal_max, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+128; memcpy(bptr, &dsr->h1.cal_min, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+132; memcpy(bptr, &dsr->h1.slice_duration, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+136; memcpy(bptr, &dsr->h1.toffset, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+140; memcpy(bptr, &dsr->h1.glmax, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+144; memcpy(bptr, &dsr->h1.glmin, 4); if(!same_order) swawbip(bptr, 4);
 
    bptr=buf+148; memcpy(bptr, dsr->h1.descrip, 80);
    bptr=buf+228; memcpy(bptr, dsr->h1.aux_file, 24);
    bptr=buf+252; memcpy(bptr, &dsr->h1.qform_code, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+254; memcpy(bptr, &dsr->h1.sform_code, 2); if(!same_order) swabip(bptr, 2);
    bptr=buf+256; memcpy(bptr, &dsr->h1.quatern_b, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+260; memcpy(bptr, &dsr->h1.quatern_c, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+264; memcpy(bptr, &dsr->h1.quatern_d, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+268; memcpy(bptr, &dsr->h1.qoffset_x, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+272; memcpy(bptr, &dsr->h1.qoffset_y, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+276; memcpy(bptr, &dsr->h1.qoffset_z, 4); if(!same_order) swawbip(bptr, 4);
    bptr=buf+280; memcpy(bptr, dsr->h1.srow_x, 16); if(!same_order) swawbip(bptr, 16);
    bptr=buf+296; memcpy(bptr, dsr->h1.srow_y, 16); if(!same_order) swawbip(bptr, 16);
    bptr=buf+312; memcpy(bptr, dsr->h1.srow_z, 16); if(!same_order) swawbip(bptr, 16);
    bptr=buf+328; memcpy(bptr, dsr->h1.intent_name, 16);
    bptr=buf+344; memcpy(bptr, dsr->h1.magic, 4);
 
  } else {
 
    unsigned char *bptr=buf+0; memcpy(bptr, &dsr->h2.sizeof_hdr, 4); if(!same_order) swap32ip(bptr, 1);
    bptr=buf+4; memcpy(bptr, &dsr->h2.magic, 8);
    bptr=buf+12; memcpy(bptr, &dsr->h2.datatype, 2); if(!same_order) swap16ip(bptr, 1);
    bptr=buf+14; memcpy(bptr, &dsr->h2.bitpix, 2); if(!same_order) swap16ip(bptr, 1);
    bptr=buf+16; memcpy(bptr, &dsr->h2.dim, 64); if(!same_order) swap64ip(bptr, 8);
    bptr=buf+80; memcpy(bptr, &dsr->h2.intent_p1, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+88; memcpy(bptr, &dsr->h2.intent_p2, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+96; memcpy(bptr, &dsr->h2.intent_p3, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+104; memcpy(bptr, &dsr->h2.pixdim, 64); if(!same_order) swap64ip(bptr, 8);
    bptr=buf+168; memcpy(bptr, &dsr->h2.vox_offset, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+176; memcpy(bptr, &dsr->h2.scl_slope, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+184; memcpy(bptr, &dsr->h2.scl_inter, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+192; memcpy(bptr, &dsr->h2.cal_max, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+200; memcpy(bptr, &dsr->h2.cal_min, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+208; memcpy(bptr, &dsr->h2.slice_duration, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+216; memcpy(bptr, &dsr->h2.toffset, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+224; memcpy(bptr, &dsr->h2.slice_start, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+232; memcpy(bptr, &dsr->h2.slice_end, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+240; memcpy(bptr, dsr->h2.descrip, 80);
    bptr=buf+320; memcpy(bptr, dsr->h2.aux_file, 24);
    bptr=buf+344; memcpy(bptr, &dsr->h2.qform_code, 4); if(!same_order) swap32ip(bptr, 1);
    bptr=buf+348; memcpy(bptr, &dsr->h2.sform_code, 4); if(!same_order) swap32ip(bptr, 1);
    bptr=buf+352; memcpy(bptr, &dsr->h2.quatern_b, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+360; memcpy(bptr, &dsr->h2.quatern_c, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+368; memcpy(bptr, &dsr->h2.quatern_d, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+376; memcpy(bptr, &dsr->h2.qoffset_x, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+384; memcpy(bptr, &dsr->h2.qoffset_y, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+392; memcpy(bptr, &dsr->h2.qoffset_z, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+400; memcpy(bptr, dsr->h2.srow_x, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_x+1, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_x+2, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_x+3, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+432; memcpy(bptr, dsr->h2.srow_y, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_y+1, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_y+2, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_y+3, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+464; memcpy(bptr, dsr->h2.srow_z, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_z+1, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_z+2, 8); if(!same_order) swap64ip(bptr, 1);
    bptr+=8; memcpy(bptr, dsr->h2.srow_z+3, 8); if(!same_order) swap64ip(bptr, 1);
    bptr=buf+496; memcpy(bptr, &dsr->h2.slice_code, 4); if(!same_order) swap32ip(bptr, 1);
    bptr=buf+500; memcpy(bptr, &dsr->h2.xyzt_units, 4); if(!same_order) swap32ip(bptr, 1);
    bptr=buf+504; memcpy(bptr, &dsr->h2.intent_code, 4); if(!same_order) swap32ip(bptr, 1);
    bptr=buf+508; memcpy(bptr, dsr->h2.intent_name, 16);
    bptr=buf+524; memcpy(bptr, &dsr->h2.dim_info, 1);
    bptr=buf+525; memcpy(bptr, dsr->h2.unused_str, 15);
 
  }
 
  /* Open file for write */
  FILE *fp;
  if(verbose>2) printf("  opening file for write in binary mode\n");
  if(fileExist(filename) && 
     (strncmp(dsr->h1.magic, "n+1", 3)==0 || strncmp(dsr->h1.magic, "n+2", 3)==0) ) {
    /* Existing single file format NIfTI; just edit the header, do not touch the pixel data */
    fp=fopen(filename, "r+b");
  } else {
    /* Otherwise just open for write, deleting any previous content */
    fp=fopen(filename, "wb");
  }
  if(fp==NULL) return(TPCERROR_CANNOT_OPEN);
 
  /* Write buffer into the file */
  if(verbose>2) printf("  writing NIfTI header\n");
  if(fwrite(buf, 1, hdrSize, fp) != hdrSize) {
    fclose(fp); return(TPCERROR_CANNOT_WRITE);
  }
 
  /* Write extender */
  if(verbose>2) printf("  writing NIfTI extender\n");
  if(fwrite(dsr->e.extension, 1, NIFTI1_HEADER_EXTENDER_SIZE, fp) != NIFTI1_HEADER_EXTENDER_SIZE) {
    fclose(fp); return(TPCERROR_CANNOT_WRITE);
  }
 
  /* Close the file */
  fclose(fp);
 
  if(verbose>1) printf("  NIfTI header written.\n");
  return(TPCERROR_OK);
}

Referenced by imgWriteNifti().