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nii_dicom_batch.cpp
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//#define myNoSave //do not save images to disk
#ifdef _MSC_VER
#include <direct.h>
#define getcwd _getcwd
#define chdir _chrdir
#include "io.h"
//#include <math.h>
#define MiniZ
#else
#include <unistd.h>
#ifdef myDisableMiniZ
#undef MiniZ
#else
#define MiniZ
#endif
#endif
#if defined(__APPLE__) && defined(__MACH__)
#endif
#ifndef myDisableZLib
#ifdef MiniZ
#include "miniz.c" //single file clone of libz
#else
#include <zlib.h>
#endif
#else
#undef MiniZ
#endif
#include "tinydir.h"
#include "print.h"
#include "nifti1_io_core.h"
#ifndef USING_R
#include "nifti1.h"
#endif
#include "nii_dicom_batch.h"
#ifndef USING_R
#include "nii_foreign.h"
#endif
#include "nii_dicom.h"
#include "nii_ortho.h"
#ifdef myEnableJNIfTI
#include "base64.h"
#include "cJSON.h"
#endif
#include <ctype.h> //toupper
#include <float.h>
#include <math.h>
#include <stdbool.h> //requires VS 2015 or later
#include <stddef.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <time.h> // clock_t, clock, CLOCKS_PER_SEC
#if defined(_WIN64) || defined(_WIN32)
#include <windows.h> //write to registry
#endif
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
#if defined(_WIN64) || defined(_WIN32)
const char kPathSeparator = '\\';
const char kFileSep[2] = "\\";
#else
const char kPathSeparator = '/';
const char kFileSep[2] = "/";
#endif
#ifdef USING_R
#include "ImageList.h"
#undef isnan
#define isnan ISNAN
#undef isfinite
#define isfinite R_FINITE
#endif
#define newTilt
#ifdef USING_R
#ifndef max
#define max(a, b) (a > b ? a : b)
#endif
#ifndef min
#define min(a, b) (a < b ? a : b)
#endif
#else
#ifndef max
#define max(a, b) \
({ __typeof__ (a) _a = (a); \
__typeof__ (b) _b = (b); \
_a > _b ? _a : _b; })
#endif
#ifndef min
#define min(a, b) \
({ __typeof__ (a) _a = (a); \
__typeof__ (b) _b = (b); \
_a < _b ? _a : _b; })
#endif
#endif
#ifdef USING_DCM2NIIXFSWRAPPER
// create the struct to save nifti header, image data, TDICOMdata, & TDTI information.
// no .nii, .bval, .bvec are created.
MRIFSSTRUCT mrifsStruct;
// retrieve the struct
MRIFSSTRUCT* nii_getMrifsStruct()
{
return &mrifsStruct;
}
// free the memory used for the image and dti
void nii_clrMrifsStruct()
{
free(mrifsStruct.imgM);
free(mrifsStruct.tdti);
}
#endif
bool isADCnotDTI(TDTI bvec) { //returns true if bval!=0 but all bvecs == 0 (Philips code for derived ADC image)
return ((!isSameFloat(bvec.V[0], 0.0f)) && //not a B-0 image
((isSameFloat(bvec.V[1], 0.0f)) && (isSameFloat(bvec.V[2], 0.0f)) && (isSameFloat(bvec.V[3], 0.0f))));
}
struct TDCMsort {
uint64_t indx, img;
uint32_t dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS];
};
struct TSearchList {
unsigned long numItems, maxItems;
char **str;
};
#ifndef PATH_MAX
#define PATH_MAX 4096
#endif
void dropFilenameFromPath(char *path) {
const char *dirPath = strrchr(path, '/'); //UNIX
if (dirPath == 0)
dirPath = strrchr(path, '\\'); //Windows
if (dirPath == NULL) {
strcpy(path, "");
} else
path[dirPath - path] = 0; // please make sure there is enough space in TargetDirectory
if (strlen(path) == 0) { //file name did not specify path, assume relative path and return current working directory
//strcat (path,"."); //relative path - use cwd <- not sure if this works on Windows!
char cwd[PATH_MAX];
char *ok = getcwd(cwd, sizeof(cwd));
if (ok != NULL)
strcat(path, cwd);
}
}
void dropTrailingFileSep(char *path) { //
size_t len = strlen(path) - 1;
if (len <= 0)
return;
if (path[len] == '/')
path[len] = '\0';
else if (path[len] == '\\')
path[len] = '\0';
}
bool is_fileexists(const char *filename) {
FILE *fp = NULL;
if ((fp = fopen(filename, "r"))) {
fclose(fp);
return true;
}
return false;
}
#ifndef S_ISDIR
#define S_ISDIR(mode) (((mode)&S_IFMT) == S_IFDIR)
#endif
#ifndef S_ISREG
#define S_ISREG(mode) (((mode)&S_IFMT) == S_IFREG)
#endif
bool is_fileNotDir(const char *path) { //returns false if path is a folder; requires #include <sys/stat.h>
struct stat buf;
stat(path, &buf);
return S_ISREG(buf.st_mode);
} //is_file()
bool is_exe(const char *path) { //requires #include <sys/stat.h>
struct stat buf;
if (stat(path, &buf) != 0)
return false; //file does not eist
if (!S_ISREG(buf.st_mode))
return false; //not regular file, e.g. '..'
return (buf.st_mode & 0111);
//return (S_ISREG(buf.st_mode) && (buf.st_mode & 0111) );
} //is_exe()
#if defined(_WIN64) || defined(_WIN32)
//Windows does not support lstat
int is_dir(const char *pathname, int follow_link) {
struct stat s;
if ((NULL == pathname) || (0 == strlen(pathname)))
return 0;
int err = stat(pathname, &s);
if (-1 == err)
return 0; // does not exist
else {
if (S_ISDIR(s.st_mode)) {
return 1; // it's a dir
} else {
return 0; // exists but is no dir
}
}
} // is_dir()
#else //if windows else Unix
int is_dir(const char *pathname, int follow_link) {
struct stat s;
int retval;
if ((NULL == pathname) || (0 == strlen(pathname)))
return 0; // does not exist
retval = follow_link ? stat(pathname, &s) : lstat(pathname, &s);
if ((-1 != retval) && (S_ISDIR(s.st_mode)))
return 1; // it's a dir
return 0; // exists but is no dir
} // is_dir()
#endif
void opts2Prefs(struct TDCMopts *opts, struct TDCMprefs *prefs) {
setDefaultPrefs(prefs);
prefs->isVerbose = opts->isVerbose;
prefs->compressFlag = opts->compressFlag;
prefs->isIgnoreTriggerTimes = opts->isIgnoreTriggerTimes;
}
void geCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isVerbose) {
//0018,1312 phase encoding is either in row or column direction
//0043,1039 (or 0043,a039). b value (as the first number in the string).
//0019,10bb (or 0019,a0bb). phase diffusion direction
//0019,10bc (or 0019,a0bc). frequency diffusion direction
//0019,10bd (or 0019,a0bd). slice diffusion direction
//These directions are relative to freq,phase,slice, so although no
//transformations are required, you need to check the direction of the
//phase encoding. This is in DICOM message 0018,1312. If this has value
//COL then if swap the x and y value and reverse the sign on the z value.
//If the phase encoding is not COL, then just reverse the sign on the x value.
if ((d->manufacturer != kMANUFACTURER_GE) && (d->manufacturer != kMANUFACTURER_CANON))
return;
if (d->isBVecWorldCoordinates)
return; //Canon classic DICOMs use image space, enhanced use world space!
if ((!d->isEPI) && (d->CSA.numDti == 1))
d->CSA.numDti = 0; //issue449
if (d->CSA.numDti < 1)
return;
if ((toupper(d->patientOrient[0]) == 'H') && (toupper(d->patientOrient[1]) == 'F') && (toupper(d->patientOrient[2]) == 'S'))
; //participant was head first supine
else {
printMessage("GE DTI directions require head first supine acquisition\n");
return;
}
bool col = false;
if (d->phaseEncodingRC == 'C')
col = true;
else if (d->phaseEncodingRC != 'R') {
printWarning("Unable to determine DTI gradients, 0018,1312 should be either R or C");
return;
}
if (abs(sliceDir) != 3)
printWarning("Limited validation for non-Axial DTI: confirm gradient vector transformation.\n");
//GE vectors from Xiangrui Li' dicm2nii, validated with datasets from https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
ivec3 flp;
if (abs(sliceDir) == 1)
flp = setiVec3(1, 1, 0); //SAGITTAL
else if (abs(sliceDir) == 2)
flp = setiVec3(0, 1, 1); //CORONAL
else if (abs(sliceDir) == 3)
flp = setiVec3(0, 0, 1); //AXIAL
else {
printMessage("Impossible GE slice orientation!");
flp = setiVec3(0, 0, 1); //AXIAL???
}
if (sliceDir < 0)
flp.v[2] = 1 - flp.v[2];
if ((isVerbose) || (!col)) {
printMessage("Saving %d DTI gradients. GE Reorienting %s : please validate. isCol=%d sliceDir=%d flp=%d %d %d\n", d->CSA.numDti, d->protocolName, col, sliceDir, flp.v[0], flp.v[1], flp.v[2]);
if (!col)
printWarning("Reorienting for ROW phase-encoding untested.\n");
}
bool scaledBValWarning = false;
for (int i = 0; i < d->CSA.numDti; i++) {
float vLen = sqrt((vx[i].V[1] * vx[i].V[1]) + (vx[i].V[2] * vx[i].V[2]) + (vx[i].V[3] * vx[i].V[3]));
if ((vx[i].V[0] <= FLT_EPSILON) || (vLen <= FLT_EPSILON)) { //bvalue=0
for (int v = 1; v < 4; v++)
vx[i].V[v] = 0.0f;
continue; //do not normalize or reorient 0 vectors
}
if ((vLen > 0.03) && (vLen < 0.97)) {
//bVal scaled by norm(g)^2 issue163,245
float bValtemp = 0, bVal = 0, bVecScale = 0;
// rounding by 5 with minimum of 5 if b-value > 0
bValtemp = vx[i].V[0] * (vLen * vLen);
if (bValtemp > 0 && bValtemp < 5) {
bVal = 5;
} else {
bVal = (int)((bValtemp + 2.5f) / 5) * 5;
}
if (bVal == 0)
bVecScale = 0;
else {
bVecScale = sqrt((float)vx[i].V[0] / bVal);
}
if (!scaledBValWarning) {
printMessage("GE BVal scaling (e.g. %g -> %g s/mm^2)\n", vx[i].V[0], bVal);
scaledBValWarning = true;
}
vx[i].V[0] = bVal;
vx[i].V[1] = vx[i].V[1] * bVecScale;
vx[i].V[2] = vx[i].V[2] * bVecScale;
vx[i].V[3] = vx[i].V[3] * bVecScale;
}
if (!col) { //rows need to be swizzled
//see Stanford dataset Ax_DWI_Tetrahedral_7 unable to resolve between possible solutions
// http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
float swap = vx[i].V[1];
vx[i].V[1] = vx[i].V[2];
vx[i].V[2] = swap;
vx[i].V[2] = -vx[i].V[2]; //because of transpose?
}
for (int v = 0; v < 3; v++)
if (flp.v[v] == 1)
vx[i].V[v + 1] = -vx[i].V[v + 1];
vx[i].V[2] = -vx[i].V[2]; //we read out Y-direction opposite order as dicm2nii, see also opts.isFlipY
}
//These next lines are only so files appear identical to old versions of dcm2niix:
// dicm2nii and dcm2niix generate polar opposite gradient directions.
// this does not matter, since intensity is the normal of the gradient vector.
for (int i = 0; i < d->CSA.numDti; i++)
for (int v = 1; v < 4; v++)
vx[i].V[v] = -vx[i].V[v];
//These next lines convert any "-0" values to "0"
for (int i = 0; i < d->CSA.numDti; i++)
for (int v = 1; v < 4; v++)
if (isSameFloat(vx[i].V[v], -0))
vx[i].V[v] = 0.0f;
} // geCorrectBvecs()
void siemensPhilipsCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isVerbose) {
//see Matthew Robson's http://users.fmrib.ox.ac.uk/~robson/internal/Dicom2Nifti111.m
//convert DTI vectors from scanner coordinates to image frame of reference
//Uses 6 orient values from ImageOrientationPatient (0020,0037)
// requires PatientPosition 0018,5100 is HFS (head first supine)
if ((!d->isBVecWorldCoordinates) && (d->manufacturer != kMANUFACTURER_MEDISO) && (d->manufacturer != kMANUFACTURER_BRUKER) && (d->manufacturer != kMANUFACTURER_TOSHIBA) && (d->manufacturer != kMANUFACTURER_HITACHI) && (d->manufacturer != kMANUFACTURER_UIH) && (d->manufacturer != kMANUFACTURER_SIEMENS) && (d->manufacturer != kMANUFACTURER_PHILIPS))
return;
if (d->CSA.numDti < 1)
return;
if (d->manufacturer == kMANUFACTURER_UIH) {
for (int i = 0; i < d->CSA.numDti; i++) {
vx[i].V[2] = -vx[i].V[2];
for (int v = 0; v < 4; v++)
if (vx[i].V[v] == -0.0f)
vx[i].V[v] = 0.0f; //remove sign from values that are virtually zero
}
//simple diagnostics for data prior to realignment: useful as first direction is the same for al Philips sequences
//for (int i = 0; i < 3; i++)
// printf("%g = %g %g %g\n", vx[i].V[0], vx[i].V[1], vx[i].V[2], vx[i].V[3]);
return;
} //https://github.com/rordenlab/dcm2niix/issues/225
if ((toupper(d->patientOrient[0]) == 'H') && (toupper(d->patientOrient[1]) == 'F') && (toupper(d->patientOrient[2]) == 'S'))
; //participant was head first supine
else {
printMessage("Check bvecs: expected Patient Position (0018,5100) to be 'HFS' not '%s'\n", d->patientOrient);
//return; //see https://github.com/rordenlab/dcm2niix/issues/238
}
vec3 read_vector = setVec3(d->orient[1], d->orient[2], d->orient[3]);
vec3 phase_vector = setVec3(d->orient[4], d->orient[5], d->orient[6]);
vec3 slice_vector = crossProduct(read_vector, phase_vector);
read_vector = nifti_vect33_norm(read_vector);
phase_vector = nifti_vect33_norm(phase_vector);
slice_vector = nifti_vect33_norm(slice_vector);
for (int i = 0; i < d->CSA.numDti; i++) {
float vLen = sqrt((vx[i].V[1] * vx[i].V[1]) + (vx[i].V[2] * vx[i].V[2]) + (vx[i].V[3] * vx[i].V[3]));
if ((vx[i].V[0] <= FLT_EPSILON) || (vLen <= FLT_EPSILON)) { //bvalue=0
if ((vx[i].V[0] > 50.0) && (!d->isDerived)) //Philip stores n.b. UIH B=1.25126 Vec=0,0,0 while Philips stored isotropic images
printWarning("Volume %d appears to be derived image ADC/Isotropic (non-zero b-value with zero vector length)\n", i);
continue; //do not normalize or reorient b0 vectors
} //if bvalue=0
vec3 bvecs_old = setVec3(vx[i].V[1], vx[i].V[2], vx[i].V[3]);
vec3 bvecs_new = setVec3(dotProduct(bvecs_old, read_vector), dotProduct(bvecs_old, phase_vector), dotProduct(bvecs_old, slice_vector));
bvecs_new = nifti_vect33_norm(bvecs_new);
vx[i].V[1] = bvecs_new.v[0];
vx[i].V[2] = -bvecs_new.v[1];
vx[i].V[3] = bvecs_new.v[2];
if (abs(sliceDir) == kSliceOrientMosaicNegativeDeterminant)
vx[i].V[2] = -vx[i].V[2];
for (int v = 0; v < 4; v++)
if (vx[i].V[v] == -0.0f)
vx[i].V[v] = 0.0f; //remove sign from values that are virtually zero
} //for each direction
if (d->isVectorFromBMatrix) {
printWarning("Saving %d DTI gradients. Eddy users: B-matrix does not encode b-vector polarity (issue 265).\n", d->CSA.numDti);
} else if (abs(sliceDir) == kSliceOrientMosaicNegativeDeterminant) {
printWarning("Saving %d DTI gradients. Validate vectors (matrix had a negative determinant).\n", d->CSA.numDti); //perhaps Siemens sagittal
} else if ((d->sliceOrient == kSliceOrientTra) || (d->manufacturer != kMANUFACTURER_PHILIPS)) {
if (isVerbose)
printMessage("Saving %d DTI gradients. Validate vectors.\n", d->CSA.numDti);
} else if (d->sliceOrient == kSliceOrientUnknown)
printWarning("Saving %d DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n", d->CSA.numDti);
if (d->manufacturer == kMANUFACTURER_BRUKER)
printWarning("Bruker DTI support experimental (issue 265).\n");
} // siemensPhilipsCorrectBvecs()
bool isNanPosition(struct TDICOMdata d) { //in 2007 some Siemens RGB DICOMs did not include the PatientPosition 0020,0032 tag
if (isnan(d.patientPosition[1]))
return true;
if (isnan(d.patientPosition[2]))
return true;
if (isnan(d.patientPosition[3]))
return true;
return false;
} // isNanPosition()
bool isSamePosition(struct TDICOMdata d, struct TDICOMdata d2) {
if (isNanPosition(d) || isNanPosition(d2))
return false;
if (!isSameFloat(d.patientPosition[1], d2.patientPosition[1]))
return false;
if (!isSameFloat(d.patientPosition[2], d2.patientPosition[2]))
return false;
if (!isSameFloat(d.patientPosition[3], d2.patientPosition[3]))
return false;
return true;
} // isSamePosition()
void nii_saveText(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts, struct nifti_1_header *h, char *dcmname) {
if (!opts.isCreateText)
return;
char txtname[2048] = {""};
strcpy(txtname, pathoutname);
strcat(txtname, ".txt");
//printMessage("Saving text %s\n",txtname);
FILE *fp = fopen(txtname, "w");
fprintf(fp, "%s\tField Strength:\t%g\tProtocolName:\t%s\tScanningSequence00180020:\t%s\tTE:\t%g\tTR:\t%g\tSeriesNum:\t%ld\tAcquNum:\t%d\tImageNum:\t%d\tImageComments:\t%s\tDateTime:\t%f\tName:\t%s\tConvVers:\t%s\tDoB:\t%s\tGender:\t%c\tAge:\t%s\tDimXYZT:\t%d\t%d\t%d\t%d\tCoil:\t%d\tEchoNum:\t%d\tOrient(6)\t%g\t%g\t%g\t%g\t%g\t%g\tbitsAllocated\t%d\tInputName\t%s\n",
pathoutname, d.fieldStrength, d.protocolName, d.scanningSequence, d.TE, d.TR, d.seriesNum, d.acquNum, d.imageNum, d.imageComments,
d.dateTime, d.patientName, kDCMvers, d.patientBirthDate, d.patientSex, d.patientAge, h->dim[1], h->dim[2], h->dim[3], h->dim[4],
d.coilCrc, d.echoNum, d.orient[1], d.orient[2], d.orient[3], d.orient[4], d.orient[5], d.orient[6],
d.bitsAllocated, dcmname);
fclose(fp);
} // nii_saveText()
#define myReadAsciiCsa
#ifdef myReadAsciiCsa
//read from the ASCII portion of the Siemens CSA series header
// this is not recommended: poorly documented
// it is better to stick to the binary portion of the Siemens CSA image header
#if defined(_WIN64) || defined(_WIN32) || defined(__sun) || (defined(__APPLE__) && defined(__POWERPC__))
//https://opensource.apple.com/source/Libc/Libc-1044.1.2/string/FreeBSD/memmem.c
/*-
* Copyright (c) 2005 Pascal Gloor <[email protected]>
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
* 3. The name of the author may not be used to endorse or promote
* products derived from this software without specific prior written
* permission.
*
* THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
* OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
*/
const void *memmem(const char *l, size_t l_len, const char *s, size_t s_len) {
char *cur, *last;
const char *cl = (const char *)l;
const char *cs = (const char *)s;
/* we need something to compare */
if (l_len == 0 || s_len == 0)
return NULL;
/* "s" must be smaller or equal to "l" */
if (l_len < s_len)
return NULL;
/* special case where s_len == 1 */
if (s_len == 1)
return memchr(l, (int)*cs, l_len);
/* the last position where its possible to find "s" in "l" */
last = (char *)cl + l_len - s_len;
for (cur = (char *)cl; cur <= last; cur++)
if (cur[0] == cs[0] && memcmp(cur, cs, s_len) == 0)
return cur;
return NULL;
}
//n.b. memchr returns "const void *" not "void *" for Windows C++ https://msdn.microsoft.com/en-us/library/d7zdhf37.aspx
#endif //for systems without memmem
int readKeyN1(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
if (!keyPos)
return -1;
int ret = 0;
int i = (int)strlen(key);
while ((i < remLength) && (keyPos[i] != 0x0A)) {
if (keyPos[i] >= '0' && keyPos[i] <= '9')
ret = (10 * ret) + keyPos[i] - '0';
i++;
}
return ret;
} //readKeyN1() //return -1 if key not found
int readKey(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
int ret = 0;
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
if (!keyPos)
return ret;
int i = (int)strlen(key);
while ((i < remLength) && (keyPos[i] != 0x0A)) {
if (keyPos[i] >= '0' && keyPos[i] <= '9')
ret = (10 * ret) + keyPos[i] - '0';
i++;
}
return ret;
} //readKey() //return 0 if key not found
float readKeyFloatNan(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
if (!keyPos)
return NAN;
char str[kDICOMStr];
strcpy(str, "");
char tmpstr[2];
tmpstr[1] = 0;
int i = (int)strlen(key);
while ((i < remLength) && (keyPos[i] != 0x0A)) {
if ((keyPos[i] >= '0' && keyPos[i] <= '9') || (keyPos[i] == '.') || (keyPos[i] == '-')) {
tmpstr[0] = keyPos[i];
strcat(str, tmpstr);
}
i++;
}
if (strlen(str) < 1)
return NAN;
return atof(str);
} //readKeyFloatNan()
float readKeyFloat(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
if (!keyPos)
return 0.0;
char str[kDICOMStr];
strcpy(str, "");
char tmpstr[2];
tmpstr[1] = 0;
int i = (int)strlen(key);
while ((i < remLength) && (keyPos[i] != 0x0A)) {
if ((keyPos[i] >= '0' && keyPos[i] <= '9') || (keyPos[i] == '.') || (keyPos[i] == '-')) {
tmpstr[0] = keyPos[i];
strcat(str, tmpstr);
}
i++;
}
if (strlen(str) < 1)
return 0.0;
return atof(str);
} //readKeyFloat()
void readKeyStr(const char *key, char *buffer, int remLength, char *outStr) {
//if key is CoilElementID.tCoilID the string 'CoilElementID.tCoilID = ""Head_32""' returns 'Head32'
strcpy(outStr, "");
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
if (!keyPos)
return;
int i = (int)strlen(key);
int outLen = 0;
char tmpstr[2];
tmpstr[1] = 0;
bool isQuote = false;
while ((i < remLength) && (keyPos[i] != 0x0A)) {
if ((isQuote) && (keyPos[i] != '"') && (outLen < kDICOMStrLarge)) {
tmpstr[0] = keyPos[i];
strcat(outStr, tmpstr);
outLen++;
}
if (keyPos[i] == '"') {
if (outLen > 0)
break;
isQuote = true;
}
i++;
}
} //readKeyStr()
int phoenixOffsetCSASeriesHeader(unsigned char *buff, int lLength) {
//returns offset to ASCII Phoenix data
if (lLength < 36)
return 0;
if ((buff[0] != 'S') || (buff[1] != 'V') || (buff[2] != '1') || (buff[3] != '0'))
return EXIT_FAILURE;
int lPos = 8; //skip 8 bytes of data, 'SV10' plus 2 32-bit values unused1 and unused2
int lnTag = buff[lPos] + (buff[lPos + 1] << 8) + (buff[lPos + 2] << 16) + (buff[lPos + 3] << 24);
if ((buff[lPos + 4] != 77) || (lnTag < 1))
return 0;
lPos += 8; //skip 8 bytes of data, 32-bit lnTag plus 77 00 00 0
TCSAtag tagCSA;
TCSAitem itemCSA;
for (int lT = 1; lT <= lnTag; lT++) {
memcpy(&tagCSA, &buff[lPos], sizeof(tagCSA)); //read tag
if (!littleEndianPlatform())
nifti_swap_4bytes(1, &tagCSA.nitems);
if (tagCSA.nitems > 128) {
printError("%d n_tags CSA Series Header corrupted (0029,1020 ) see issue 633.\n", tagCSA.nitems);
return EXIT_FAILURE;
}
//printf("%d CSA of %s %d\n",lPos, tagCSA.name, tagCSA.nitems);
lPos += sizeof(tagCSA);
if (strcmp(tagCSA.name, "MrPhoenixProtocol") == 0)
return lPos;
for (int lI = 1; lI <= tagCSA.nitems; lI++) {
memcpy(&itemCSA, &buff[lPos], sizeof(itemCSA));
lPos += sizeof(itemCSA);
if (!littleEndianPlatform())
nifti_swap_4bytes(1, &itemCSA.xx2_Len);
lPos += ((itemCSA.xx2_Len + 3) / 4) * 4;
}
}
return 0;
} //phoenixOffsetCSASeriesHeader()
#define kMaxWipFree 64
typedef struct {
float TE0, TE1, delayTimeInTR, phaseOversampling, phaseResolution, txRefAmp, accelFactTotal;
int phaseEncodingLines, existUcImageNumb, ucMode, baseResolution, interp, partialFourier, echoSpacing,
difBipolar, parallelReductionFactorInPlane, refLinesPE, combineMode, patMode, ucMTC, accelFact3D;
float alFree[kMaxWipFree];
float adFree[kMaxWipFree];
float alTI[kMaxWipFree];
float sPostLabelingDelay, ulLabelingDuration, dAveragesDouble, dThickness, ulShape, sPositionDTra, sNormalDTra;
} TCsaAscii;
void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, int csaLength, float *shimSetting, char *coilID, char *consistencyInfo, char *coilElements, char *pulseSequenceDetails, char *fmriExternalInfo, char *protocolName, char *wipMemBlock) {
//reads ASCII portion of CSASeriesHeaderInfo and returns lEchoTrainDuration or lEchoSpacing value
// returns 0 if no value found
csaAscii->sPostLabelingDelay = 0.0;
csaAscii->ulLabelingDuration = 0.0;
csaAscii->TE0 = 0.0;
csaAscii->TE1 = 0.0;
csaAscii->delayTimeInTR = -0.001;
csaAscii->phaseOversampling = 0.0;
csaAscii->phaseResolution = 0.0;
csaAscii->txRefAmp = 0.0;
csaAscii->phaseEncodingLines = 0;
csaAscii->existUcImageNumb = 0;
csaAscii->ucMode = -1;
csaAscii->baseResolution = 0;
csaAscii->interp = 0;
csaAscii->partialFourier = 0;
csaAscii->echoSpacing = 0;
csaAscii->difBipolar = 0; //0=not assigned,1=bipolar,2=monopolar
csaAscii->parallelReductionFactorInPlane = 0;
csaAscii->accelFact3D = 0;//lAccelFact3D
csaAscii->accelFactTotal = 0.0;
csaAscii->refLinesPE = 0;
csaAscii->combineMode = 0;
csaAscii->patMode = 0;
csaAscii->ucMTC = 0;
for (int i = 0; i < 8; i++)
shimSetting[i] = 0.0;
strcpy(coilID, "");
strcpy(consistencyInfo, "");
strcpy(coilElements, "");
strcpy(pulseSequenceDetails, "");
strcpy(fmriExternalInfo, "");
strcpy(wipMemBlock, "");
strcpy(protocolName, "");
if ((csaOffset < 0) || (csaLength < 8))
return;
FILE *pFile = fopen(filename, "rb");
if (pFile == NULL)
return;
fseek(pFile, 0, SEEK_END);
long lSize = ftell(pFile);
if (lSize < (csaOffset + csaLength)) {
fclose(pFile);
return;
}
fseek(pFile, csaOffset, SEEK_SET);
char *buffer = (char *)malloc(csaLength);
if (buffer == NULL)
return;
size_t result = fread(buffer, 1, csaLength, pFile);
if ((int)result != csaLength)
return;
fclose(pFile);
//next bit complicated: restrict to ASCII portion to avoid buffer overflow errors in BINARY portion
int startAscii = phoenixOffsetCSASeriesHeader((unsigned char *)buffer, csaLength);
//n.b. previous function parses binary V* "SV10" portion of header
// it will return "EXIT_FAILURE for text based X* "<XProtocol>"
int csaLengthTrim = csaLength;
char *bufferTrim = buffer;
if ((startAscii > 0) && (startAscii < csaLengthTrim)) { //ignore binary data at start
bufferTrim += startAscii;
csaLengthTrim -= startAscii;
}
char keyStr[] = "### ASCCONV BEGIN"; //skip to start of ASCII often "### ASCCONV BEGIN ###" but also "### ASCCONV BEGIN object=MrProtDataImpl@MrProtocolData"
char *keyPos = (char *)memmem(bufferTrim, csaLengthTrim, keyStr, strlen(keyStr));
if (keyPos) {
//We could detect multi-echo MPRAGE here, e.g. "lContrasts = 4"- but ideally we want an earlier detection
csaLengthTrim -= (keyPos - bufferTrim);
//FmriExternalInfo listed AFTER AscConvEnd and uses different delimiter ||
// char keyStrExt[] = "FmriExternalInfo";
// readKeyStr(keyStrExt, keyPos, csaLengthTrim, fmriExternalInfo);
#define myCropAtAscConvEnd
#ifdef myCropAtAscConvEnd
char keyStrEnd[] = "### ASCCONV END";
char *keyPosEnd = (char *)memmem(keyPos, csaLengthTrim, keyStrEnd, strlen(keyStrEnd));
if ((keyPosEnd) && ((keyPosEnd - keyPos) < csaLengthTrim)) //ignore binary data at end
csaLengthTrim = (int)(keyPosEnd - keyPos);
#endif
char keyStrLns[] = "sKSpace.lPhaseEncodingLines";
csaAscii->phaseEncodingLines = readKey(keyStrLns, keyPos, csaLengthTrim);
char keyStrUcImg[] = "sSliceArray.ucImageNumb";
csaAscii->existUcImageNumb = readKey(keyStrUcImg, keyPos, csaLengthTrim);
char keyStrUcMode[] = "sSliceArray.ucMode";
csaAscii->ucMode = readKeyN1(keyStrUcMode, keyPos, csaLengthTrim);
char keyStrBase[] = "sKSpace.lBaseResolution";
csaAscii->baseResolution = readKey(keyStrBase, keyPos, csaLengthTrim);
char keyStrInterp[] = "sKSpace.uc2DInterpolation";
csaAscii->interp = readKey(keyStrInterp, keyPos, csaLengthTrim);
char keyStrPF[] = "sKSpace.ucPhasePartialFourier";
csaAscii->partialFourier = readKey(keyStrPF, keyPos, csaLengthTrim);
char keyStrES[] = "sFastImaging.lEchoSpacing";
csaAscii->echoSpacing = readKey(keyStrES, keyPos, csaLengthTrim);
char keyStrDS[] = "sDiffusion.dsScheme";
csaAscii->difBipolar = readKey(keyStrDS, keyPos, csaLengthTrim);
if (csaAscii->difBipolar == 0) {
char keyStrROM[] = "ucReadOutMode";
csaAscii->difBipolar = readKey(keyStrROM, keyPos, csaLengthTrim);
if ((csaAscii->difBipolar >= 1) && (csaAscii->difBipolar <= 2)) { //E11C Siemens/CMRR dsScheme: 1=bipolar, 2=unipolar, B17 CMRR ucReadOutMode 0x1=monopolar, 0x2=bipolar
csaAscii->difBipolar = 3 - csaAscii->difBipolar;
} //https://github.com/poldracklab/fmriprep/pull/1359#issuecomment-448379329
}
char keyStrAF[] = "sPat.lAccelFactPE";
csaAscii->parallelReductionFactorInPlane = readKey(keyStrAF, keyPos, csaLengthTrim);
char keyStrAF3D[] = "sPat.lAccelFact3D";
csaAscii->accelFact3D = readKey(keyStrAF3D, keyPos, csaLengthTrim);
char keyStrAFTotal[] = "sPat.dTotalAccelFact";
csaAscii->accelFactTotal = readKeyFloat(keyStrAFTotal, keyPos, csaLengthTrim);
//issue 672: the tag "sSliceAcceleration.lMultiBandFactor" is not reliable:
// series 7 dcm_qa_xa30 has x3 multiband, but this tag reports "1" (perhaps cmrr sequences)
//char keyStrMB[] = "sSliceAcceleration.lMultiBandFactor";
//csaAscii->multiBandFactor = readKey(keyStrMB, keyPos, csaLengthTrim);
char keyStrRef[] = "sPat.lRefLinesPE";
csaAscii->refLinesPE = readKey(keyStrRef, keyPos, csaLengthTrim);
char keyStrCombineMode[] = "ucCoilCombineMode";
csaAscii->combineMode = readKeyN1(keyStrCombineMode, keyPos, csaLengthTrim);
//BIDS CoilCombinationMethod <- Siemens 'Coil Combine Mode' CSA ucCoilCombineMode 1 = Sum of Squares, 2 = Adaptive Combine,
//printf("CoilCombineMode %d\n", csaAscii->combineMode);
char keyStrPATMode[] = "sPat.ucPATMode"; //n.b. field set even if PAT not enabled, e.g. will list SENSE for a R-factor of 1
csaAscii->patMode = readKeyN1(keyStrPATMode, keyPos, csaLengthTrim);
char keyStrucMTC[] = "sPrepPulses.ucMTC"; //n.b. field set even if PAT not enabled, e.g. will list SENSE for a R-factor of 1
csaAscii->ucMTC = readKeyN1(keyStrucMTC, keyPos, csaLengthTrim);
//printf("PATMODE %d\n", csaAscii->patMode);
//char keyStrETD[] = "sFastImaging.lEchoTrainDuration";
//*echoTrainDuration = readKey(keyStrETD, keyPos, csaLengthTrim);
//char keyStrEF[] = "sFastImaging.lEPIFactor";
//ret = readKey(keyStrEF, keyPos, csaLengthTrim);
char keyStrCoil[] = "sCoilElementID.tCoilID";
readKeyStr(keyStrCoil, keyPos, csaLengthTrim, coilID);
char keyStrCI[] = "sProtConsistencyInfo.tMeasuredBaselineString";
readKeyStr(keyStrCI, keyPos, csaLengthTrim, consistencyInfo);
char keyStrCS[] = "sCoilSelectMeas.sCoilStringForConversion";
readKeyStr(keyStrCS, keyPos, csaLengthTrim, coilElements);
char keyStrSeq[] = "tSequenceFileName";
readKeyStr(keyStrSeq, keyPos, csaLengthTrim, pulseSequenceDetails);
char keyStrWipMemBlock[] = "sWipMemBlock.tFree";
readKeyStr(keyStrWipMemBlock, keyPos, csaLengthTrim, wipMemBlock);
char keyStrPn[] = "tProtocolName";
readKeyStr(keyStrPn, keyPos, csaLengthTrim, protocolName);
char keyStrTE0[] = "alTE[0]";
csaAscii->TE0 = readKeyFloatNan(keyStrTE0, keyPos, csaLengthTrim);
char keyStrTE1[] = "alTE[1]";
csaAscii->TE1 = readKeyFloatNan(keyStrTE1, keyPos, csaLengthTrim);
char keyStrPLD[] = "sAsl.sPostLabelingDelay[0]";
csaAscii->sPostLabelingDelay = readKeyFloatNan(keyStrPLD, keyPos, csaLengthTrim);
char keyStrLD[] = "sAsl.ulLabelingDuration";
csaAscii->ulLabelingDuration = readKeyFloatNan(keyStrLD, keyPos, csaLengthTrim);
//read ALL alTI[*] values
for (int k = 0; k < kMaxWipFree; k++)
csaAscii->alTI[k] = NAN;
char keyStrTiFree[] = "alTI[";
//check if ANY csaAscii.alFree tags exist
char *keyPosTi = (char *)memmem(keyPos, csaLengthTrim, keyStrTiFree, strlen(keyStrTiFree));
if (keyPosTi) {
for (int k = 0; k < kMaxWipFree; k++) {
char txt[1024] = {""};
snprintf(txt, 1024, "%s%d]", keyStrTiFree, k);
csaAscii->alTI[k] = readKeyFloatNan(txt, keyPos, csaLengthTrim);
}
}
//read ALL csaAscii.alFree[*] values
for (int k = 0; k < kMaxWipFree; k++)
csaAscii->alFree[k] = 0.0;
char keyStrAlFree[] = "sWipMemBlock.alFree[";
//check if ANY csaAscii.alFree tags exist
char *keyPosFree = (char *)memmem(keyPos, csaLengthTrim, keyStrAlFree, strlen(keyStrAlFree));
if (keyPosFree) {
for (int k = 0; k < kMaxWipFree; k++) {
char txt[1024] = {""};
snprintf(txt, 1024, "%s%d]", keyStrAlFree, k);
csaAscii->alFree[k] = readKeyFloat(txt, keyPos, csaLengthTrim);
}
}
//read ALL csaAscii.adFree[*] values
for (int k = 0; k < kMaxWipFree; k++)
csaAscii->adFree[k] = NAN;
char keyStrAdFree[50];
strcpy(keyStrAdFree, "sWipMemBlock.adFree[");
//char keyStrAdFree[] = "sWipMemBlock.adFree[";
//check if ANY csaAscii.adFree tags exist
keyPosFree = (char *)memmem(keyPos, csaLengthTrim, keyStrAdFree, strlen(keyStrAdFree));
if (!keyPosFree) { //"Wip" -> "WiP", modern -> old Siemens
strcpy(keyStrAdFree, "sWiPMemBlock.adFree[");
keyPosFree = (char *)memmem(keyPos, csaLengthTrim, keyStrAdFree, strlen(keyStrAdFree));
}
if (keyPosFree) {
for (int k = 0; k < kMaxWipFree; k++) {
char txt[1024] = {""};
snprintf(txt, 1024, "%s%d]", keyStrAdFree, k);
csaAscii->adFree[k] = readKeyFloatNan(txt, keyPos, csaLengthTrim);
}
}
//read labelling plane
char keyStrDThickness[] = "sRSatArray.asElm[1].dThickness";
csaAscii->dThickness = readKeyFloat(keyStrDThickness, keyPos, csaLengthTrim);
if (csaAscii->dThickness > 0.0) {
char keyStrUlShape[] = "sRSatArray.asElm[1].ulShape";
csaAscii->ulShape = readKeyFloat(keyStrUlShape, keyPos, csaLengthTrim);
char keyStrSPositionDTra[] = "sRSatArray.asElm[1].sPosition.dTra";
csaAscii->sPositionDTra = readKeyFloat(keyStrSPositionDTra, keyPos, csaLengthTrim);
char keyStrSNormalDTra[] = "sRSatArray.asElm[1].sNormal.dTra";
csaAscii->sNormalDTra = readKeyFloat(keyStrSNormalDTra, keyPos, csaLengthTrim);
}
//Read NEX number of averages
char keyStrDAveragesDouble[] = "dAveragesDouble";
csaAscii->dAveragesDouble = readKeyFloat(keyStrDAveragesDouble, keyPos, csaLengthTrim);
//read delay time
char keyStrDelay[] = "lDelayTimeInTR";
csaAscii->delayTimeInTR = readKeyFloat(keyStrDelay, keyPos, csaLengthTrim);
char keyStrOver[] = "sKSpace.dPhaseOversamplingForDialog";
csaAscii->phaseOversampling = readKeyFloat(keyStrOver, keyPos, csaLengthTrim);
char keyStrPhase[] = "sKSpace.dPhaseResolution";
csaAscii->phaseResolution = readKeyFloat(keyStrPhase, keyPos, csaLengthTrim);
char keyStrAmp[] = "sTXSPEC.asNucleusInfo[0].flReferenceAmplitude";
csaAscii->txRefAmp = readKeyFloat(keyStrAmp, keyPos, csaLengthTrim);
//lower order shims: newer sequences
char keyStrSh0[] = "sGRADSPEC.asGPAData[0].lOffsetX";
shimSetting[0] = readKeyFloat(keyStrSh0, keyPos, csaLengthTrim);
char keyStrSh1[] = "sGRADSPEC.asGPAData[0].lOffsetY";
shimSetting[1] = readKeyFloat(keyStrSh1, keyPos, csaLengthTrim);
char keyStrSh2[] = "sGRADSPEC.asGPAData[0].lOffsetZ";
shimSetting[2] = readKeyFloat(keyStrSh2, keyPos, csaLengthTrim);
//lower order shims: older sequences
char keyStrSh0s[] = "sGRADSPEC.lOffsetX";
if (shimSetting[0] == 0.0)
shimSetting[0] = readKeyFloat(keyStrSh0s, keyPos, csaLengthTrim);
char keyStrSh1s[] = "sGRADSPEC.lOffsetY";
if (shimSetting[1] == 0.0)
shimSetting[1] = readKeyFloat(keyStrSh1s, keyPos, csaLengthTrim);
char keyStrSh2s[] = "sGRADSPEC.lOffsetZ";
if (shimSetting[2] == 0.0)
shimSetting[2] = readKeyFloat(keyStrSh2s, keyPos, csaLengthTrim);
//higher order shims: older sequences
char keyStrSh3[] = "sGRADSPEC.alShimCurrent[0]";
shimSetting[3] = readKeyFloat(keyStrSh3, keyPos, csaLengthTrim);
char keyStrSh4[] = "sGRADSPEC.alShimCurrent[1]";
shimSetting[4] = readKeyFloat(keyStrSh4, keyPos, csaLengthTrim);
char keyStrSh5[] = "sGRADSPEC.alShimCurrent[2]";
shimSetting[5] = readKeyFloat(keyStrSh5, keyPos, csaLengthTrim);
char keyStrSh6[] = "sGRADSPEC.alShimCurrent[3]";
shimSetting[6] = readKeyFloat(keyStrSh6, keyPos, csaLengthTrim);
char keyStrSh7[] = "sGRADSPEC.alShimCurrent[4]";
shimSetting[7] = readKeyFloat(keyStrSh7, keyPos, csaLengthTrim);
}
free(buffer);
return;
} // siemensCsaAscii()
#endif //myReadAsciiCsa()
#ifndef myDisableZLib
//Uncomment next line to decode GE Protocol Data Block, for caveats see https://github.com/rordenlab/dcm2niix/issues/163
#define myReadGeProtocolBlock
#endif
#ifdef myReadGeProtocolBlock
int geProtocolBlock(const char *filename, int geOffset, int geLength, int isVerbose, int *sliceOrder, int *viewOrder, int *mbAccel, int *nSlices, float *groupDelay, char ioptGE[]) {
*sliceOrder = -1;
*viewOrder = 0;
*mbAccel = 0;
*nSlices = 0;
*groupDelay = 0.0;
int ret = EXIT_FAILURE;
if ((geOffset < 0) || (geLength < 20))
return ret;
FILE *pFile = fopen(filename, "rb");
if (pFile == NULL)
return ret;
fseek(pFile, 0, SEEK_END);
long lSize = ftell(pFile);
if (lSize < (geOffset + geLength)) {
fclose(pFile);
return ret;
}
fseek(pFile, geOffset, SEEK_SET);
uint8_t *pCmp = (uint8_t *)malloc(geLength); //uint8_t -> mz_uint8
if (pCmp == NULL)
return ret;
size_t result = fread(pCmp, 1, geLength, pFile);
if ((int)result != geLength)
return ret;
int cmpSz = geLength;
//http://www.forensicswiki.org/wiki/Gzip
// always little endia! http://www.onicos.com/staff/iz/formats/gzip.html
if (cmpSz < 20)
return ret;
if ((pCmp[0] != 31) || (pCmp[1] != 139) || (pCmp[2] != 8))
return ret; //check signature and deflate algorithm
uint8_t flags = pCmp[3];
bool isFNAME = ((flags & 0x08) == 0x08);
bool isFCOMMENT = ((flags & 0x10) == 0x10);
int hdrSz = 10;
if (isFNAME) { //skip null-terminated string FNAME
for (; hdrSz < cmpSz; hdrSz++)
if (pCmp[hdrSz] == 0)
break;
hdrSz++;
}
if (isFCOMMENT) { //skip null-terminated string COMMENT
for (; hdrSz < cmpSz; hdrSz++)
if (pCmp[hdrSz] == 0)
break;
hdrSz++;
}
uint32_t unCmpSz = ((uint32_t)pCmp[cmpSz - 4]) + ((uint32_t)pCmp[cmpSz - 3] << 8) + ((uint32_t)pCmp[cmpSz - 2] << 16) + ((uint32_t)pCmp[cmpSz - 1] << 24);
//printf(">> %d %d %zu %zu %zu\n", isFNAME, isFCOMMENT, cmpSz, unCmpSz, hdrSz);
z_stream s;
memset(&s, 0, sizeof(z_stream));
#ifdef myDisableMiniZ
#define MZ_DEFAULT_WINDOW_BITS 15 // Window bits
#endif
inflateInit2(&s, -MZ_DEFAULT_WINDOW_BITS);
uint8_t *pUnCmp = (uint8_t *)malloc((size_t)unCmpSz);
s.avail_out = unCmpSz;
s.next_in = pCmp + hdrSz;
s.avail_in = cmpSz - hdrSz - 8;
s.next_out = (uint8_t *)pUnCmp;
#ifdef myDisableMiniZ
ret = inflate(&s, Z_SYNC_FLUSH);
if (ret != Z_STREAM_END) {
free(pUnCmp);
return EXIT_FAILURE;
}
#else
ret = mz_inflate(&s, MZ_SYNC_FLUSH);
if (ret != MZ_STREAM_END) {
free(pUnCmp);
return EXIT_FAILURE;
}
#endif
//https://groups.google.com/forum/#!msg/comp.protocols.dicom/mxnCkv8A-i4/W_uc6SxLwHQJ
// DISCOVERY MR750 / 24\MX\MR Software release:DV24.0_R01_1344.a) are now storing an XML file
// <?xml version="1.0" encoding="UTF-8"?>
if ((pUnCmp[0] == '<') && (pUnCmp[1] == '?'))
printWarning("New XML-based GE Protocol Block is not yet supported: please report issue on dcm2niix Github page\n");
char keyStrSO[] = "SLICEORDER";
*sliceOrder = readKeyN1(keyStrSO, (char *)pUnCmp, unCmpSz);
char keyStrVO[] = "VIEWORDER";
*viewOrder = readKey(keyStrVO, (char *)pUnCmp, unCmpSz);
char keyStrMB[] = "MBACCEL";