Experimental solution for issue 384 (#384)

FILENAMING.md

@@ -44,7 +44,7 @@ In general dcm2niix creates images with 3D dimensions, or 4 dimensions when the
  - _MoCo is appended to the ProtocolName if Image Type (0008,0008) includes the term 'MOCO'. This helps disambiguate Siemens fMRI runs where both motion corrected and raw data is stored for a single session.
  - _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) 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) or trigger time (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).
  - _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.
 
 Some post-fixes are specific to Philips DICOMs

README.md

@@ -121,6 +121,7 @@ The following tools exploit dcm2niix
   - [brainnetome DiffusionKit](http://diffusion.brainnetome.org/en/latest/) uses dcm2niix to convert images.
   - [Brain imAgiNg Analysis iN Arcana (Banana)](https://pypi.org/project/banana/) is a collection of brain imaging analysis workflows, it uses dcm2niix for format conversions.
   - [BOLD5000_autoencoder](https://github.com/nmningmei/BOLD5000_autoencoder) uses dcm2niix to pipe imaging data into an unsupervised machine learning algorithm.
+  - [clinica](https://github.com/aramis-lab/clinica) is a software platform for clinical neuroimaging studies that uses dcm2niix to convert DICOM images.
   - [dcm2niix can help convert data from the Adolescent Brain Cognitive Development (ABCD) DICOM to BIDS](https://github.com/ABCD-STUDY/abcd-dicom2bids)
   - [bidsify](https://github.com/spinoza-rec/bidsify) is a Python project that uses dcm2niix to convert DICOM and Philips PAR/REC images to the BIDS standard.
   - [bidskit](https://github.com/jmtyszka/bidskit) uses dcm2niix to create [BIDS](http://bids.neuroimaging.io/) datasets.
@@ -139,6 +140,7 @@ The following tools exploit dcm2niix
   - [fsleyes](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes) is a powerful Python-based image viewer. It uses dcm2niix to handle DICOM files through its fslpy libraries.
   - [Functional Real-Time Interactive Endogenous Neuromodulation and Decoding (FRIEND) Engine](https://github.com/InstitutoDOr/FriendENGINE) uses dcm2niix.
   - [heudiconv](https://github.com/nipy/heudiconv) can use dcm2niix to create [BIDS](http://bids.neuroimaging.io/) datasets.
+  - [kipettools](https://github.com/mathesong/kipettools) uses dcm2niix to load PET data.
   - [LEAD-DBS](http://www.lead-dbs.org/) uses dcm2niix for [DICOM import](https://github.com/leaddbs/leaddbs/blob/master/ea_dicom_import.m).
   - [MRIcroGL](https://github.com/neurolabusc/MRIcroGL) is available for MacOS, Linux and Windows and provides a graphical interface for dcm2niix. You can get compiled copies from the [MRIcroGL NITRC web site](https://www.nitrc.org/projects/mricrogl/).
   - [neurodocker](https://github.com/kaczmarj/neurodocker) includes dcm2niix as a lean, minimal install Dockerfile.
@@ -147,7 +149,7 @@ The following tools exploit dcm2niix
   - [neurodocker](https://github.com/kaczmarj/neurodocker) generates [custom](https://github.com/rordenlab/dcm2niix/issues/138) Dockerfiles given specific versions of neuroimaging software.
   - [NeuroElf](http://neuroelf.net) can use dcm2niix to convert DICOM images.
   - [Neuroinformatics Database (NiDB)](https://github.com/gbook/nidb) is designed to store, retrieve, analyze, and share neuroimaging data. It uses dcm2niix for image QA and handling some formats. 
-  - [NiftyPET](https://niftypet.readthedocs.io/en/latest/intro.htmlNiftyPET) provides PET image reconstruction and analysis, and uses dcm2niix to handle DICOM images. 
+  - [NiftyPET](https://niftypet.readthedocs.io/en/latest/install.html) provides PET image reconstruction and analysis, and uses dcm2niix to handle DICOM images. 
   - [nipype](https://github.com/nipy/nipype) can use dcm2niix to convert images.
   - [PNL-nipype](https://github.com/pnlbwh/Dummy-PNL-nipype) is a Python script that can convert dcm2niix created NIfTI files to the popular NRRD format (including DWI gradient tables). Note, recent versions of dcm2niix can directly convert DICOM images to NRRD.
   - [pydcm2niix is a Python module for working with dcm2niix](https://github.com/jstutters/pydcm2niix).

console/main_console.cpp

@@ -106,7 +106,7 @@ void showHelp(const char * argv[], struct TDCMopts opts) {
     #if !defined(_WIN64) && !defined(_WIN32) //shell script for Unix only
 	printf("  -u : up-to-date check\n");
 	#endif
-	printf("  -v : verbose (n/y or 0/1/2 [no, yes, logorrheic], default 0)\n");
+	printf("  -v : verbose (n/y or 0/1/2, default 0) [no, yes, logorrheic]\n");
 //#define kNAME_CONFLICT_SKIP 0 //0 = write nothing for a file that exists with desired name
 //#define kNAME_CONFLICT_OVERWRITE 1 //1 = overwrite existing file with same name
 //#define kNAME_CONFLICT_ADD_SUFFIX 2 //default 2 = write with new suffix as a new file

console/nii_dicom.cpp

@@ -4350,6 +4350,7 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );
 double TE = 0.0; //most recent echo time recorded
 	bool is2005140FSQ = false;
 	bool isDICOMANON = false; //issue383
+	bool isMATLAB = false; //issue383
 	//double contentTime = 0.0;
 	int echoTrainLengthPhil = 0;
 	int philMRImageDiffBValueNumber = 0;
@@ -4873,10 +4874,11 @@ double TE = 0.0; //most recent echo time recorded
                 char impTxt[kDICOMStr];
                 dcmStr (lLength, &buffer[lPos], impTxt);
                 int slen = (int) strlen(impTxt);
-				//if ((slen > 5) && (strstr(impTxt, "dcm4che") != NULL) )
-				//	isDcm4Che = true;
+				if ((slen > 5) && (strstr(impTxt, "MATLAB") != NULL) )
+					isMATLAB = true;
 				if((slen < 5) || (strstr(impTxt, "XA10A") == NULL) ) break;
 				d.isXA10A = true;
+
             	break; }
             case kSourceApplicationEntityTitle: {
             	char saeTxt[kDICOMStr];
@@ -5148,16 +5150,19 @@ double TE = 0.0; //most recent echo time recorded
                 break; }
             case kInversionTimes : {//issue 380
                 if ((lLength < 8) || ((lLength % 8) != 0)) break;
-            	int nTI = lLength / 8;
             	d.TI = dcmFloatDouble(lLength, &buffer[lPos], d.isLittleEndian);
+            	/*
+            	//see issue385 : Philips reports Implausible InversionTimes
+            	int nTI = lLength / 8;
             	if (nTI > 1) {
             		bool isTIvaries = false; 
                 	for (int i = 1; i < nTI; i++) {
         				float ti = dcmFloatDouble(8, &buffer[lPos+(i*8)],d.isLittleEndian);
         				if (!isSameFloatGE(ti, d.TI)) isTIvaries = true;	
         			} 
-        			if (isTIvaries) printWarning("0018,9079 reports multiple inversion times.\n");
+        			if (isTIvaries) printWarning("0018,9079 reports multiple inversion times: %s\n", fname); 
 				}
+				*/
                 break; }
             case kPartialFourier : //(0018,9081) CS [YES],[NO]
 				if (lLength < 2) break;
@@ -5539,15 +5544,16 @@ double TE = 0.0; //most recent echo time recorded
             case kImagingFrequency :
             	d.imagingFrequency = dcmStrFloat(lLength, &buffer[lPos]);
                 break;
-           	case kTriggerTime:
+           	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;            	
+            	if ((d.manufacturer != kMANUFACTURER_GE) && (d.manufacturer != kMANUFACTURER_PHILIPS)) break; //issue384            	
             	d.triggerDelayTime = dcmStrFloat(lLength, &buffer[lPos]); //???? issue 336
+            	if (d.manufacturer != kMANUFACTURER_GE) break;            	
             	d.CSA.sliceTiming[acquisitionTimesGE_UIH] = d.triggerDelayTime;
                 //printf("%g\n", d.CSA.sliceTiming[acquisitionTimesGE_UIH]);
 				acquisitionTimesGE_UIH ++;
-				break;
+				break; }
             case kEffectiveTE : {
             	TE = dcmFloatDouble(lLength, &buffer[lPos], d.isLittleEndian);
             	if (d.TE <= 0.0)
@@ -6721,7 +6727,7 @@ if (d.isHasPhase)
 		strcpy(d.seriesInstanceUID, d.studyInstanceUID);
 		d.seriesUidCrc = mz_crc32X((unsigned char*) &d.protocolName, strlen(d.protocolName));
 	}
-	if (isDICOMANON) {
+	if ((isDICOMANON) && (isMATLAB)) {
 		//issue 383
 		d.seriesInstanceUID[0] = '\0';
 		strcat(d.seriesInstanceUID, d.studyDate);

console/nii_dicom_batch.cpp

@@ -1353,7 +1353,7 @@ tse3d: T2*/
 		json_Str(fp, "\t\"ReceiveCoilActiveElements\": \"%s\",\n", d.coilElements);
 		if (strcmp(d.coilElements,d.coilName) != 0)
 			json_Str(fp, "\t\"CoilString\": \"%s\",\n", d.coilName);
-		if ((!d.is3DAcq) && (d.phaseEncodingLines > d.echoTrainLength) && (d.echoTrainLength > 1)) {
+		if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (!d.is3DAcq) && (d.phaseEncodingLines > d.echoTrainLength) && (d.echoTrainLength > 1)) {
 				//ETL is > 1, as some GE files list 1, as an example see series mr_0005 in dcm_qa_nih
 				float pf = (float)d.phaseEncodingLines;
 				if (d.accelFactPE > 1)
@@ -2451,7 +2451,7 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt
     	sprintf(newstr, "_t%d", (int)roundf(dcm.triggerDelayTime));
         strcat (outname,newstr);
     }
-	//could add (isAddNamePostFixes) to these next two, but consequences could be catastrophic
+    //could add (isAddNamePostFixes) to these next two, but consequences could be catastrophic
     if (dcm.isRawDataStorage) //avoid name clash for Philips XX_ files
     	strcat (outname,"_Raw");
     if (dcm.isGrayscaleSoftcopyPresentationState) //avoid name clash for Philips PS_ files
@@ -4634,7 +4634,8 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
     if (nConvert > 1) {
         //next: detect trigger time see example https://www.slicer.org/wiki/Documentation/4.4/Modules/MultiVolumeExplorer
         double triggerDx = dcmList[dcmSort[nConvert-1].indx].triggerDelayTime - dcmList[indx0].triggerDelayTime;
-        dcmList[indx0].triggerDelayTime = triggerDx;
+        if (triggerDx > 0.0) //issue 384
+        	dcmList[indx0].triggerDelayTime = triggerDx;
         //next: determine gantry tilt
         if (dcmList[indx0].gantryTilt != 0.0f)
             printWarning("Note these images have gantry tilt of %g degrees (manufacturer ID = %d)\n", dcmList[indx0].gantryTilt, dcmList[indx0].manufacturer);
@@ -5365,7 +5366,7 @@ int isSameFloatDouble (double a, double b) {
 }
 
 struct TWarnings { //generate a warning only once per set
-        bool acqNumVaries, bitDepthVaries, dateTimeVaries, echoVaries, phaseVaries, coilVaries, forceStackSeries, seriesUidVaries, nameVaries, nameEmpty, orientVaries;
+        bool acqNumVaries, bitDepthVaries, dateTimeVaries, echoVaries, triggerVaries, phaseVaries, coilVaries, forceStackSeries, seriesUidVaries, nameVaries, nameEmpty, orientVaries;
 };
 
 TWarnings setWarnings() {
@@ -5375,6 +5376,7 @@ TWarnings setWarnings() {
 	r.dateTimeVaries = false;
 	r.phaseVaries = false;
 	r.echoVaries = false;
+	r.triggerVaries = false;
 	r.coilVaries = false;
 	r.seriesUidVaries = false;
 	r.forceStackSeries = false;
@@ -5463,6 +5465,12 @@ bool isSameSet (struct TDICOMdata d1, struct TDICOMdata d2, struct TDCMopts* opt
         *isMultiEcho = true;
         return false;
     }
+    if ((d1.triggerDelayTime != d2.triggerDelayTime) && (d1.manufacturer == kMANUFACTURER_PHILIPS)) { //issue 384
+        if (!warnings->triggerVaries)
+        	printMessage("Slices not stacked: trigger time varies\n");
+        warnings->triggerVaries = true;
+        return false;
+    }
     if (d1.coilCrc != d2.coilCrc) {
         if (!warnings->coilVaries)
         	printMessage("Slices not stacked: coil varies\n");