Detect GE Multi-Band (#336)

FILENAMING.md

@@ -36,7 +36,7 @@ In general dcm2niix creates images with 3D dimensions, or 4 dimensions when the
  - _imaginary imaginary component of complex image
  - _real real component of complex image
  - _phMag rare case where phase and magnitude are saved as the 4th dimension
- - _t  If the trigger delay time (0020,9153 or 0018,1060) is non-zero, it will be recorded in the file name. For example, the files "T1_t178.nii" and "T1_t511" suggests that the T1 scan was acquired with two cardiac trigger delays (178 and 511ms after the last R-peak).
+ - _t  If the trigger delay time (0020,9153) is non-zero, it will be recorded in the file name. For example, the files "T1_t178.nii" and "T1_t511" suggests that the T1 scan was acquired with two cardiac trigger delays (178 and 511ms after the last R-peak).
  - _ADC Philips specific case. A DWI image where derived isotropic, ADC or trace volume was appended to the series. Since this image will disrupt subsequent processing, and because subsequent processing (dwidenoise, topup, eddy) will yield better derived images, dcm2niix will also create an additional image without this volume. Therefore, the _ADC file should typically be discarded. If you want dcm2niix to discard these useless derived images, use the ignore feature ('-i y').
  - _Eq is specific to [CT scans](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Computed_Tomography_.28CT.2C_CAT.29). These scans can be acquired with variable distance between the slices of a 3D volume. NIfTI asumes all 2D slices that form a 3D stack are equidistant. Therefore, dcm2niix reslices the input data to generate an equidistant volume.
  - _Tilt is specific to [CT scans](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Computed_Tomography_.28CT.2C_CAT.29). These scans can be acquired with a gantry tilt that causes a skew that can not be stored in a NIfTI qForm. Therefore, the slices are resampled to remove the effect of tilt.
@@ -64,4 +64,6 @@ dcm2niix will attempt to write your image using the naming scheme you specify wi
 | (vertical bar or pipe)
 ? (question mark)
 * (asterisk)
-```
+```
+
+Be warned that dcm2niix will copy all allowed characters verbatim, which can cause problems for some other tools. Consider this [sample dataset](https://github.com/neurolabusc/dcm_qa_nih/tree/master/In/20180918GE/mr_0004) where the DICOM Protocol Name (0018,1030) is 'Axial_EPI-FMRI_(Interleaved_I_to_S)'. The parentheses ("round brackets") may cause other tools issues. Consider converting this series with the command 'dcm2niix -f %s_%p ~/DICOM' to create the file '4_Axial_EPI-FMRI_(Interleaved_I_to_S).nii'.If you now run the command 'fslhd 4_Axial_EPI-FMRI_(Interleaved_I_to_S).nii' you will get the error '-bash: syntax error near unexpected token `(''. Therefore, it is often a good idea to use double quotes to specify the names of files. In this example 'fslhd "4_Axial_EPI-FMRI_(Interleaved_I_to_S).nii"' will work correctly.

console/nii_dicom.cpp

@@ -5370,8 +5370,8 @@ double TE = 0.0; //most recent echo time recorded
            	case kTriggerTime:
 				//untested method to detect slice timing for GE PSD “epi” with multiphase option
 				// will not work for current PSD “epiRT” (BrainWave RT, fMRI/DTI package provided by Medical Numerics)
-            	if (d.manufacturer != kMANUFACTURER_GE) break;
-            	d.triggerDelayTime = dcmStrFloat(lLength, &buffer[lPos]);
+            	if (d.manufacturer != kMANUFACTURER_GE) break;            	
+            	d.triggerDelayTime = dcmStrFloat(lLength, &buffer[lPos]); //???? issue 336
             	d.CSA.sliceTiming[acquisitionTimesGE_UIH] = d.triggerDelayTime;
                 //printf("%g\n", d.CSA.sliceTiming[acquisitionTimesGE_UIH]);
 				acquisitionTimesGE_UIH ++;

console/nii_dicom.h

@@ -43,7 +43,7 @@ extern "C" {
 	#define kCCsuf " CompilerNA" //unknown compiler!
 #endif
 
-#define kDCMdate "v1.0.20190910"
+#define kDCMdate "v1.0.20190926"
 #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf
 
 static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic

console/nii_dicom_batch.cpp

@@ -766,7 +766,7 @@ void siemensCsaAscii(const char * filename, TCsaAscii* csaAscii, int csaOffset,
  #define myReadGeProtocolBlock
 #endif
 #ifdef myReadGeProtocolBlock
-int  geProtocolBlock(const char * filename,  int geOffset, int geLength, int isVerbose, int* sliceOrder, int* viewOrder) {
+int  geProtocolBlock(const char * filename,  int geOffset, int geLength, int isVerbose, int* sliceOrder, int* viewOrder, int* mbAccel) {
 	*sliceOrder = -1;
 	*viewOrder = 0;
 	int ret = EXIT_FAILURE;
@@ -836,8 +836,10 @@ int  geProtocolBlock(const char * filename,  int geOffset, int geLength, int isV
 		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"; //"MATRIXX";
+	char keyStrVO[] = "VIEWORDER"; 
 	*viewOrder  = readKey(keyStrVO, (char *) pUnCmp, unCmpSz);
+	char keyStrMB[] = "MBACCEL";
+	*mbAccel  = readKey(keyStrMB, (char *) pUnCmp, unCmpSz);
 	if (isVerbose > 1) {
 		printMessage("GE Protocol Block %s bytes %d compressed, %d uncompressed @ %d\n", filename, geLength, unCmpSz, geOffset);
 		printMessage(" ViewOrder %d SliceOrder %d\n", *viewOrder, *sliceOrder);
@@ -2368,7 +2370,7 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt
     	if (dcm.isHasMagnitude)
     		strcat (outname,"Mag"); //Philips enhanced with BOTH phase and Magnitude in single file
     }
-    if (dcm.triggerDelayTime >= 1) {
+    if ((dcm.triggerDelayTime >= 1) && (dcm.manufacturer != kMANUFACTURER_GE)){ //issue 336 GE uses this for slice timing
     	sprintf(newstr, "_t%d", (int)roundf(dcm.triggerDelayTime));
         strcat (outname,newstr);
     }
@@ -4236,7 +4238,6 @@ void rescueSliceTimingGE(struct TDICOMdata * d, int verbose, int nSL, const char
 	// if both of these methods fail, we can often guess based on slice order stored in the Private Protocol Data Block (0025,101B)
 	// this is referred to as "rescue" as we only know the TR, not the TA. So assumes continuous scans with no gap
 	if (d->is3DAcq) return; //no need for slice times
-	if (d->CSA.sliceTiming[0] >= 0.0) return; //slice times calculated
 	if (nSL < 2) return;
 	if (d->manufacturer != kMANUFACTURER_GE) return;
 	if ((d->protocolBlockStartGE < 1) || (d->protocolBlockLengthGE < 19)) return;
@@ -4247,12 +4248,22 @@ void rescueSliceTimingGE(struct TDICOMdata * d, int verbose, int nSL, const char
 	// Therefore, we warning the user that we are guessing
 	int viewOrderGE = -1;
 	int sliceOrderGE = -1;
+	int mbAccel = -1;
 	//printWarning("Using GE Protocol Data Block for BIDS data (beware: new feature)\n");
-	int ok = geProtocolBlock(filename, d->protocolBlockStartGE, d->protocolBlockLengthGE, verbose, &sliceOrderGE, &viewOrderGE);
+	int ok = geProtocolBlock(filename, d->protocolBlockStartGE, d->protocolBlockLengthGE, verbose, &sliceOrderGE, &viewOrderGE, &mbAccel);
 	if (ok != EXIT_SUCCESS) {
 		printWarning("Unable to decode GE protocol block\n");
 		return;
 	}
+	if (mbAccel > 1) {
+		d->CSA.multiBandFactor = mbAccel;
+		printWarning("Unabled to compute slice times for GE multi-band. SliceOrder=%d (seq=0, int=1)\n", sliceOrderGE);
+		d->CSA.sliceTiming[0] = -1.0;
+		return;
+
+	}
+	if (d->CSA.sliceTiming[0] >= 0.0) return; //slice times calculated - moved here to detect multiband, see issue 336
+
 	if ((sliceOrderGE < 0) || (sliceOrderGE > 1)) return;
 	// 0=sequential/1=interleaved
 	printWarning("Guessing slice times using ProtocolBlock SliceOrder=%d (seq=0, int=1)\n", sliceOrderGE);