Experimental start for reproin support

BIDS/README.md

@@ -82,6 +82,7 @@ These fields are present regardless of modality (e.g. MR, CT, PET).
 | PatientPosition          |      | DICOM tag 0020,0032 | D          |
 | ProcedureStepDescription |      | DICOM tag 0040,0254 | D          |
 | SoftwareVersions         |      | DICOM tag 0020,1020 | B          |
+| StudyDescription         |      | DICOM tag 0008,1030 | D          |
 | SeriesDescription        |      | DICOM tag 0008,103E | D          |
 | ProtocolName             |      | DICOM tag 0018,1030 | D          |
 | ScanningSequence         |      | DICOM tag 0018,0020 | B          |

console/nii_dicom.cpp

@@ -772,6 +772,7 @@ struct TDICOMdata clear_dicom_data() {
 	strcpy(d.deviceSerialNumber, "");
 	strcpy(d.softwareVersions, "");
 	strcpy(d.stationName, "");
+	strcpy(d.studyDescription, "");
 	strcpy(d.scanOptions, "");
 	//strcpy(d.mrAcquisitionType, "");
 	strcpy(d.seriesInstanceUID, "");
@@ -4368,6 +4369,7 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 #define kTracerRadionuclide1 0x0008 + (0x0100 << 16) //SH
 #define kTracerRadionuclide2 0x0008 + (0x0104 << 16) //LO
 #define kStationName 0x0008 + (0x1010 << 16)
+#define kStudyDescription 0x0008 + (0x1030 << 16) //LO
 #define kSeriesDescription 0x0008 + (0x103E << 16) // '0008' '103E' 'LO' 'SeriesDescription'
 #define kInstitutionalDepartmentName 0x0008 + (0x1040 << 16)
 #define kManufacturersModelName 0x0008 + (0x1090 << 16)
@@ -5695,6 +5697,9 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 		case kStationName:
 			dcmStr(lLength, &buffer[lPos], d.stationName);
 			break;
+		case kStudyDescription:
+			dcmStr(lLength, &buffer[lPos], d.studyDescription);
+			break;
 		case kSeriesDescription:
 			dcmStr(lLength, &buffer[lPos], d.seriesDescription);
 #ifdef USING_DCM2NIIXFSWRAPPER

console/nii_dicom.h

@@ -248,7 +248,7 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;
         float pixelPaddingValue;  // used for both FloatPixelPaddingValue (0028, 0122) and PixelPaddingValue (0028, 0120); NaN if not present.
         double imagingFrequency, acquisitionDuration, triggerDelayTime, RWVScale, RWVIntercept, dateTime, acquisitionTime, acquisitionDate, bandwidthPerPixelPhaseEncode;
         char parallelAcquisitionTechnique[kDICOMStr], radiopharmaceutical[kDICOMStr], convolutionKernel[kDICOMStr], unitsPT[kDICOMStr], tracerRadionuclide[kDICOMStr], decayCorrection[kDICOMStr], attenuationCorrectionMethod[kDICOMStr],reconstructionMethod[kDICOMStr], transferSyntax[kDICOMStr];
-        char prescanReuseString[kDICOMStr], imageOrientationText[kDICOMStr], pulseSequenceName[kDICOMStr], coilElements[kDICOMStr], coilName[kDICOMStr], phaseEncodingDirectionDisplayedUIH[kDICOMStr], imageBaseName[kDICOMStr], stationName[kDICOMStr], softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], instanceUID[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[kDICOMStr], imageTypeText[kDICOMStr], imageType[kDICOMStr], institutionalDepartmentName[kDICOMStr], manufacturersModelName[kDICOMStr], patientID[kDICOMStr], patientOrient[kDICOMStr], patientName[kDICOMStr], accessionNumber[kDICOMStr], seriesDescription[kDICOMStr], studyID[kDICOMStr], sequenceName[kDICOMStr], protocolName[kDICOMStr],sequenceVariant[kDICOMStr],scanningSequence[kDICOMStr], patientBirthDate[kDICOMStr], patientAge[kDICOMStr],  studyDate[kDICOMStr],studyTime[kDICOMStr];
+        char prescanReuseString[kDICOMStr], imageOrientationText[kDICOMStr], pulseSequenceName[kDICOMStr], coilElements[kDICOMStr], coilName[kDICOMStr], phaseEncodingDirectionDisplayedUIH[kDICOMStr], imageBaseName[kDICOMStr], stationName[kDICOMStr], studyDescription[kDICOMStr],  softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], instanceUID[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[kDICOMStr], imageTypeText[kDICOMStr], imageType[kDICOMStr], institutionalDepartmentName[kDICOMStr], manufacturersModelName[kDICOMStr], patientID[kDICOMStr], patientOrient[kDICOMStr], patientName[kDICOMStr], accessionNumber[kDICOMStr], seriesDescription[kDICOMStr], studyID[kDICOMStr], sequenceName[kDICOMStr], protocolName[kDICOMStr],sequenceVariant[kDICOMStr],scanningSequence[kDICOMStr], patientBirthDate[kDICOMStr], patientAge[kDICOMStr],  studyDate[kDICOMStr],studyTime[kDICOMStr];
         char deepLearningText[kDICOMStrLarge], scanOptions[kDICOMStrLarge], institutionAddress[kDICOMStrLarge], imageComments[kDICOMStrLarge];
         uint32_t dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS];
         struct TCSAdata CSA;

console/nii_dicom_batch.cpp

@@ -1395,6 +1395,7 @@ tse3d: T2*/
 		fprintf(fp, "\t\"MRAcquisitionType\": \"2D\",\n");
 	if (d.is3DAcq)
 		fprintf(fp, "\t\"MRAcquisitionType\": \"3D\",\n");
+	json_Str(fp, "\t\"StudyDescription\": \"%s\",\n", d.studyDescription);
 	json_Str(fp, "\t\"SeriesDescription\": \"%s\",\n", d.seriesDescription);
 	json_Str(fp, "\t\"ProtocolName\": \"%s\",\n", d.protocolName);
 	json_Str(fp, "\t\"ScanningSequence\": \"%s\",\n", d.scanningSequence);
@@ -3416,6 +3417,66 @@ void cleanISO8859(char *cString) {
 		}
 }
 
+void heudiconvStrPth(char *cString) {
+	int len = strlen(cString);
+	int j = 0;
+	int i = 0;
+	bool hasCaret = false;
+	while (i < len) {
+		if (cString[i] == '^') {
+			cString[j++] = kPathSeparator;
+			hasCaret = true;
+		} else if ((!hasCaret) && (cString[i] == '_') ) {
+			cString[j++] = kPathSeparator;
+		} else if (cString[i] != '-') {
+			cString[j] = cString[i];
+			j ++;
+		}
+		i++;
+	}
+	cString[j] = '\0';
+}
+
+void heudiconvStr(char *cString) {
+	int len = strlen(cString);
+	int j = 0;
+	int i = 0;
+	const char kTempPathSeparator = '\a';
+	bool hasCaret = false;
+	while (i < len) {
+		if (cString[i] != '-') {
+			cString[j] = cString[i];
+			j ++;
+		}
+		i++;
+	}
+	cString[j] = '\0';
+}
+
+void mkDirs(char *pth) {
+	if (strlen(pth) < 1) return;
+	char newdir[2048] = {""};
+	for (size_t pos = 0; pos < strlen(pth); pos++) {
+		if (pth[pos] == kPathSeparator) {
+			if (!is_dir(newdir, true))
+#if defined(_WIN64) || defined(_WIN32)
+				mkdir(newdir);
+#else
+				mkdir(newdir, 0700);
+#endif
+		}
+		char ch[128] = {""};
+		snprintf(ch, 128, "%c", pth[pos]);
+		strcat(newdir, ch);
+	}
+	if (!is_dir(newdir, true))
+#if defined(_WIN64) || defined(_WIN32)
+		mkdir(newdir);
+#else
+		mkdir(newdir, 0700);
+#endif
+} //mkDirs()
+
 void createDummyBidsBoilerplate(char *pth, bool isFunc) {
 	//https://remi-gau.github.io/bids_cookbook/#starters
 	char pathSep[2] = {"a"};
@@ -3539,13 +3600,30 @@ int nii_createFilename(struct TDICOMdata dcm, char *niiFilename, struct TDCMopts
 				strcat(outname, opts.indirParent);
 			if (f == 'G')
 				strcat(outname, dcm.accessionNumber);
-			if (f == 'H') {
-				printWarning("hazardous (%%h) bids naming experimental\n");
+			if ((f == 'H') || (f == 'V')) {
+				printWarning("hazardous (%%h) or volatile (%%v) bids naming experimental\n");
+				bool isReproin = (f == 'V');
+				if (isReproin) {
+					//https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html
+					//reproin convention is hard for one-pass, as `ses` may only be reported in one series in the session (e.g. localizer)
+					//printf("study %s\n", dcm.studyDescription);
+					//printf("series %s\n", dcm.seriesDescription);
+					//printf("id %s\n", dcm.patientID);
+					snprintf(newstr, PATH_MAX, "%s", dcm.studyDescription);
+					heudiconvStrPth(newstr);
+					if ((strlen(pth) > 0) && (pth[strlen(pth)-1] != kPathSeparator))
+						strcat(pth, kFileSep);//kPathSeparator);
+					strcat(pth, newstr);
+					mkDirs(pth);
+					strcpy(opts.bidsSubject, dcm.patientID);
+					heudiconvStr(opts.bidsSubject);
+				}
 				char bidsSubject[kOptsStr] = "sub-";
 				if (strlen(opts.bidsSubject) <= 0)
 					strcat(bidsSubject, "1");
 				else
 					strcat(bidsSubject, opts.bidsSubject);
+				printf("%s<<<:::\n", bidsSubject);
 				char bidsSession[kOptsStr] = "ses-";
 				if (strlen(opts.bidsSession) <= 0)
 					strcat(bidsSession, "1");
@@ -3626,13 +3704,13 @@ int nii_createFilename(struct TDICOMdata dcm, char *niiFilename, struct TDCMopts
 				if (strlen(dcm.protocolName) < 1)
 					printWarning("Unable to append protocol name (0018,1030) to filename (it is empty).\n");
 			}
+			if (f == 'Q')
+				strcat(outname, dcm.scanningSequence);
 			if (f == 'R') {
 				snprintf(newstr, PATH_MAX, "%d", dcm.imageNum);
 				strcat(outname, newstr);
 				isImageNumReported = true;
 			}
-			if (f == 'Q')
-				strcat(outname, dcm.scanningSequence);
 			if (f == 'S') {
 				snprintf(newstr, PATH_MAX, "%ld", dcm.seriesNum);
 				strcat(outname, newstr);