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nifti1_read_write.c
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nifti1_read_write.c
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/*********************************************************************
*
* Very simple code snippets to read/write nifti1 files
* This code is placed in the public domain.
*
* If you are the type who doesn't want to use a file format unless
* you can write your own i/o code in less than 30minutes, this
* example is for you.
*
* This code does not deal with wrong-endian data, compressed data,
* the new qform/sform orientation codes, parsing filenames, volume-
* wise or timecourse-wise data access or any of a million other very useful
* things that are in the niftilib i/o reference libraries.
* We encourage people to use the niftilib reference library and send
* feedback/suggestions, see http://niftilib.sourceforge.net/
* But, if that is too much to tackle and you just want to jump in, this
* code is a starting point.
* This code was written for maximum readability, not for the greatest
* coding style.
*
*
* If you are already a little familiar with reading/writing Analyze
* files of some flavor, and maybe even have some of your own code, here
* are the most important things to be aware of in transitioning to nifti1:
*
* 1. nii vs .hdr/.img
* nifti1 datasets can be stored either in .hdr/.img pairs of files
* or in 1 .nii file. In a .nii file the data will start at the byte
* specified by the vox_offset field, which will be 352 if no extensions
* have been added. And, nifti1 really does like that magic field set
* to "n+1" for .nii and "ni1" for .img/.hdr
*
* 2. scaling
* nifti1 datasets can contain a scaling factor. You need to check the
* scl_slope field and if that isn't 0, scale your data by
* Y * scl_slope + scl_inter
*
* 3. extensions
* nifti1 datasets can have some "extension data" stuffed after the
* regular header. You can just ignore it, but, be aware that a
* .hdr file may be longer than 348 bytes, and, in a .nii file
* you can't just jump to byte 352, you need to use the vox_offset
* field to get the start of the image data.
*
* 4. new datatypes
* nifti1 added a few new datatypes that were not in the Analyze 7.5
* format from which nifti1 is derived. If you're just working with
* your own data this is not an issue but if you get a foreign nifti1
* file, be aware of exotic datatypes like DT_COMPLEX256 and mundane
* things like DT_UINT16.
*
* 5. other stuff
* nifti1 really does like the dim[0] field set to the number of
* dimensions of the dataset. Other Analyze flavors might not
* have been so scrupulous about that.
* nifti1 has a bunch of other new fields such as intent codes,
* qform/sform, etc. but, if you just want to get your hands on
* the data blob you can ignore these. Example use of these fields
* is in the niftilib reference libraries.
*
*
*
* To compile:
* You need to put a copy of the nifti1.h header file in this directory.
* It can be obtained from the NIFTI homepage http://nifti.nimh.nih.gov/
* or from the niftilib SourceForge site http://niftilib.sourceforge.net/
*
* cc -o nifti1_read_write nifti1_read_write.c
*
*
* To run:
* nifti1_read_write -w abc.nii abc.nii
* nifti1_read_write -r abc.nii abc.nii
*
*
* The read method is hardcoded to read float32 data. To change
* to your datatype, just change the line:
* typedef float MY_DATATYPE;
*
* The write method is hardcoded to write float32 data. To change
* to your datatype, change the line:
* typedef float MY_DATATYPE;
* and change the lines:
* hdr.datatype = NIFTI_TYPE_FLOAT32;
* hdr.bitpix = 32;
*
*
* Written by Kate Fissell, University of Pittsburgh, May 2005.
*
*********************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "nifti1.h"
typedef float MY_DATATYPE;
#define MIN_HEADER_SIZE 348
#define NII_HEADER_SIZE 352
/**********************************************************************
*
* read_nifti_file
*
**********************************************************************/
static int read_nifti_file(char * const hdr_file, char * const data_file)
{
nifti_1_header hdr;
FILE *fp;
int ret,i;
double total;
MY_DATATYPE *data=NULL;
/********** open and read header */
fp = fopen(hdr_file,"r");
if (fp == NULL) {
fprintf(stderr, "\nError opening header file %s\n",hdr_file);
exit(1);
}
ret = fread(&hdr, MIN_HEADER_SIZE, 1, fp);
if (ret != 1) {
fprintf(stderr, "\nError reading header file %s\n",hdr_file);
exit(1);
}
fclose(fp);
/********** print a little header information */
fprintf(stderr, "\n%s header information:",hdr_file);
fprintf(stderr, "\nXYZT dimensions: %d %d %d %d",hdr.dim[1],hdr.dim[2],hdr.dim[3],hdr.dim[4]);
fprintf(stderr, "\nDatatype code and bits/pixel: %d %d",hdr.datatype,hdr.bitpix);
fprintf(stderr, "\nScaling slope and intercept: %.6f %.6f",hdr.scl_slope,hdr.scl_inter);
fprintf(stderr, "\nByte offset to data in datafile: %ld",(long)(hdr.vox_offset));
fprintf(stderr, "\n");
/********** open the datafile, jump to data offset */
fp = fopen(data_file,"r");
if (fp == NULL) {
fprintf(stderr, "\nError opening data file %s\n",data_file);
exit(1);
}
ret = fseek(fp, (long)(hdr.vox_offset), SEEK_SET);
if (ret != 0) {
fprintf(stderr, "\nError doing fseek() to %ld in data file %s\n",(long)(hdr.vox_offset), data_file);
exit(1);
}
/********** allocate buffer and read first 3D volume from data file */
data = (MY_DATATYPE *) malloc(sizeof(MY_DATATYPE) * hdr.dim[1]*hdr.dim[2]*hdr.dim[3]);
if (data == NULL) {
fprintf(stderr, "\nError allocating data buffer for %s\n",data_file);
exit(1);
}
ret = fread(data, sizeof(MY_DATATYPE), hdr.dim[1]*hdr.dim[2]*hdr.dim[3], fp);
if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]) {
fprintf(stderr, "\nError reading volume 1 from %s (%d)\n",data_file,ret);
exit(1);
}
fclose(fp);
/********** scale the data buffer */
if (hdr.scl_slope != 0) {
for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]; i++)
data[i] = (data[i] * hdr.scl_slope) + hdr.scl_inter;
}
/********** print mean of data */
total = 0;
for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]; i++)
total += data[i];
total /= (hdr.dim[1]*hdr.dim[2]*hdr.dim[3]);
fprintf(stderr, "\nMean of volume 1 in %s is %.3f\n",data_file,total);
return(0);
}
/**********************************************************************
*
* write_nifti_file
*
* write a sample nifti1 (.nii) data file
* datatype is float32
* XYZT size is 64x64x16x10
* XYZ voxel size is 1mm
* TR is 1500ms
*
**********************************************************************/
static int write_nifti_file(char * const hdr_file, char * const data_file)
{
nifti_1_header hdr;
nifti1_extender pad={0,0,0,0};
FILE *fp;
int ret,i;
MY_DATATYPE *data=NULL;
short do_nii;
/********** make sure user specified .hdr/.img or .nii/.nii */
if ( (strlen(hdr_file) < 4) || (strlen(data_file) < 4) ) {
fprintf(stderr, "\nError: write files must end with .hdr/.img or .nii/.nii extension\n");
exit(1);
}
if ( (!strncmp(hdr_file+(strlen(hdr_file)-4), ".hdr",4)) &&
(!strncmp(data_file+(strlen(data_file)-4), ".img",4)) ) {
do_nii = 0;
}
else if ( (!strncmp(hdr_file+(strlen(hdr_file)-4), ".nii",4)) &&
(!strncmp(data_file+(strlen(data_file)-4), ".nii",4)) ) {
do_nii = 1;
}
else {
fprintf(stderr, "\nError: file(s) to be written must end with .hdr/.img or .nii/.nii extension\n");
exit(1);
}
/********** fill in the minimal default header fields */
bzero((void *)&hdr, sizeof(hdr));
hdr.sizeof_hdr = MIN_HEADER_SIZE;
hdr.dim[0] = 4;
hdr.dim[1] = 64;
hdr.dim[2] = 64;
hdr.dim[3] = 16;
hdr.dim[4] = 10;
hdr.datatype = NIFTI_TYPE_FLOAT32;
hdr.bitpix = 32;
hdr.pixdim[1] = 1.0;
hdr.pixdim[2] = 1.0;
hdr.pixdim[3] = 1.0;
hdr.pixdim[4] = 1.5;
if (do_nii)
hdr.vox_offset = (float) NII_HEADER_SIZE;
else
hdr.vox_offset = (float)0;
hdr.scl_slope = 100.0;
hdr.xyzt_units = NIFTI_UNITS_MM | NIFTI_UNITS_SEC;
if (do_nii)
strncpy(hdr.magic, "n+1\0", 4);
else
strncpy(hdr.magic, "ni1\0", 4);
/********** allocate buffer and fill with dummy data */
data = (MY_DATATYPE *) malloc(sizeof(MY_DATATYPE) * hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]);
if (data == NULL) {
fprintf(stderr, "\nError allocating data buffer for %s\n",data_file);
exit(1);
}
for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]; i++)
data[i] = i / hdr.scl_slope;
/********** write first 348 bytes of header */
fp = fopen(hdr_file,"w");
if (fp == NULL) {
fprintf(stderr, "\nError opening header file %s for write\n",hdr_file);
exit(1);
}
ret = fwrite(&hdr, MIN_HEADER_SIZE, 1, fp);
if (ret != 1) {
fprintf(stderr, "\nError writing header file %s\n",hdr_file);
exit(1);
}
/********** if nii, write extender pad and image data */
if (do_nii == 1) {
ret = fwrite(&pad, 4, 1, fp);
if (ret != 1) {
fprintf(stderr, "\nError writing header file extension pad %s\n",hdr_file);
exit(1);
}
ret = fwrite(data, (size_t)(hdr.bitpix/8), hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4], fp);
if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]) {
fprintf(stderr, "\nError writing data to %s\n",hdr_file);
exit(1);
}
fclose(fp);
}
/********** if hdr/img, close .hdr and write image data to .img */
else {
fclose(fp); /* close .hdr file */
fp = fopen(data_file,"w");
if (fp == NULL) {
fprintf(stderr, "\nError opening data file %s for write\n",data_file);
exit(1);
}
ret = fwrite(data, (size_t)(hdr.bitpix/8), hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4], fp);
if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]) {
fprintf(stderr, "\nError writing data to %s\n",data_file);
exit(1);
}
fclose(fp);
}
free(data);
return(0);
}
/********** The main program for this test case */
int main(int argc, char * argv[])
{
char *hdr_file, *data_file;
short do_read=0;
short do_write=0;
/********** process commandline parameters */
if (argc != 4) {
fprintf(stderr, "\nUsage: %s <-r|-w> <header file> <data file>\n",argv[0]);
exit(1);
}
if (!strncmp(argv[1],"-r",2))
do_read=1;
else if (!strncmp(argv[1],"-w",2))
do_write=1;
else {
fprintf(stderr, "\nUsage: %s <-r|-w> <header file> <data file>\n",argv[0]);
exit(1);
}
hdr_file = argv[2];
data_file = argv[3];
/********** do the simple read or write */
if (do_read)
read_nifti_file(hdr_file, data_file);
else if (do_write)
write_nifti_file(hdr_file, data_file);
exit(0);
}