Override DICOM intensity scaling (#973)

Author: neurolabusc

console/main_console.cpp

@@ -79,7 +79,7 @@ void showHelp(const char *argv[], struct TDCMopts opts) {
 	printf("  -m : merge 2D slices from same series regardless of echo, exposure, etc. (n/y or 0/1/2, default 2) [no, yes, auto]\n");
 	printf("  -n : only convert this series CRC number - can be used up to %i times (default convert all)\n", MAX_NUM_SERIES);
 	printf("  -o : output directory (omit to save to input folder)\n");
-	printf("  -p : Philips precise float (not display) scaling (y/n, default y)\n");
+	printf("  -p : Philips precise float (not display) scaling (y/n/o, default y; o to override and ignore variable intensity scaling)\n");
 	printf("  -q : only search directory for DICOMs (y/l/n, default y) [y=show number of DICOMs found, l=additionally list DICOMs found, n=no]\n");
 	printf("  -r : rename instead of convert DICOMs (y/n, default n)\n");
 	printf("  -s : single file mode, do not convert other images in folder (y/n, default n)\n");
@@ -446,7 +446,9 @@ int main(int argc, const char *argv[]) {
 				i++;
 				if (invalidParam(i, argv))
 					return 0;
-				if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
+				if ((argv[i][0] == 'o') || (argv[i][0] == 'O'))
+					opts.isIgnoreIntensityScaling = true;
+				else if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
 					opts.isPhilipsFloatNotDisplayScaling = false;
 				else
 					opts.isPhilipsFloatNotDisplayScaling = true;

console/nii_dicom.cpp

@@ -5326,10 +5326,8 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 				d.imageStart = (int)lPos + (int)lFileOffset;
 				isBasicOffsetTable = true;
 			}
-			printf("!%d %d\n", lLength, isBasicOffsetTable );
 			if (!isBasicOffsetTable) {
 				d.imageBytes = lLength;
-				printf("!!!!%d\n", lLength );
 				if (d.offsetTableItems < kMaxSlice2D)
 					dti4D->offsetTable[d.offsetTableItems] = (int)lPos + (int)lFileOffset;
 				d.offsetTableItems ++;

console/nii_dicom_batch.cpp

@@ -2389,7 +2389,8 @@ tse3d: T2*/
 	//  FSL definition is start of first line until start of last line.
 	//  Other than the use of (n-1), the value is basically just 1.0/bandwidthPerPixelPhaseEncode.
 	//  https://github.com/rordenlab/dcm2niix/issues/130
-	if (d.manufacturer != kMANUFACTURER_UIH) // issue606
+	//  https://neurostars.org/t/error-bids-validation-after-dcm2bids-conversion-repetitiontime-and-acquisitionduration-are-mutually-exclusive/30759/13
+	if ((d.manufacturer != kMANUFACTURER_UIH) && (d.TR <= 0.0)) // issue606
 		json_Float(fp, "\t\"AcquisitionDuration\": %g,\n", d.acquisitionDuration);
 	if ((d.manufacturer == kMANUFACTURER_UIH) && (effectiveEchoSpacing <= 0.0)) // issue225, issue531
 		json_Float(fp, "\t\"TotalReadoutTime\": %g,\n", d.acquisitionDuration / 1000.0);
@@ -6669,7 +6670,6 @@ int nii_saveCrop(char *niiFilename, struct nifti_1_header hdr, unsigned char *im
 	hdrX.srow_y[3] += hdr.srow_y[2] * ventralCrop;
 	hdrX.srow_z[3] += hdr.srow_z[2] * ventralCrop;
 	//issue889 - also change origin for qform
-	//mork
 	mat44 Q44;
 	LOAD_MAT44(Q44,
 			   hdrX.srow_x[0], hdrX.srow_x[1], hdrX.srow_x[2], hdrX.srow_x[3],
@@ -8281,6 +8281,15 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata d
 #endif
 
 	struct nifti_1_header hdr0 = {0};
+	
+	if ((iVaries) && (dcmList[indx].manufacturer != kMANUFACTURER_PHILIPS) && (!opts.isPhilipsFloatNotDisplayScaling)) {
+		printWarning("Variance of DICOM slope/intercept is being ignored due to use of the `-p n` option.\n");
+		iVaries = false;
+	}
+	if ((iVaries) && (opts.isIgnoreIntensityScaling)) {
+		printWarning("Variance of DICOM slope/intercept is being ignored due to use of the `-p o` option.\n");
+		iVaries = false;
+	}
 	unsigned char *img = nii_loadImgXL(nameList->str[indx], &hdr0, dcmList[indx], iVaries, opts.compressFlag, opts.isVerbose, dti4D);
 	if (strlen(opts.imageComments) > 0) {
 		for (int i = 0; i < 24; i++)
@@ -8983,13 +8992,8 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata d
 		imgM = removeADC(&hdr0, imgM, numADC);
 		if (bppVaries)
 			printMessage("Saving as 32-bit float (bits allocated varies).\n");
-		else if (iVaries) {
-			if (!opts.isPhilipsFloatNotDisplayScaling) {
-				printWarning("Variance of DICOM slope/intercept is being ignored due to use of the `-p n` option.\n");
-				iVaries = false;
-			} else
-				printMessage("Saving as 32-bit float (slope, intercept or bits allocated varies).\n");
-		}
+		else if (iVaries)
+			printMessage("Saving as 32-bit float (slope, intercept or bits allocated varies).\n");
 #ifndef USING_R
 		// divest does not support non-NIfTI formats, and requires only one
 		// image per series, so skip this to avoid double-saving
@@ -10620,6 +10624,7 @@ void setDefaultOpts(struct TDCMopts *opts, const char *argv[]) { // either "setD
 	opts->isIgnoreDerivedAnd2D = false;
 	opts->isForceOnsetTimes = true;
 	opts->isPhilipsFloatNotDisplayScaling = true;
+	opts->isIgnoreIntensityScaling = false;
 	opts->isCrop = false;
 	opts->isRotate3DAcq = true;
 	opts->isGz = false;

console/nii_dicom_batch.h

@@ -74,7 +74,7 @@ struct TDicomSeries {
 
 struct TDCMopts {
 	bool isDumpNotConvert;
-	bool isKeepDirectionVaries, isIgnoreTriggerTimes, isTestx0021x105E, isAddNamePostFixes, isSaveNativeEndian, isOneDirAtATime, isRenameNotConvert, isSave3D, isGz, isPipedGz, isFlipY, isCreateBIDS, isSortDTIbyBVal, isAnonymizeBIDS, isOnlyBIDS, isCreateText, isForceOnsetTimes, isIgnoreDerivedAnd2D, isPhilipsFloatNotDisplayScaling, isTiltCorrect, isRGBplanar, isOnlySingleFile, isForceStackDCE, isIgnoreSeriesInstanceUID, isRotate3DAcq, isCrop, isGuessBidsFilename;
+	bool isKeepDirectionVaries, isIgnoreTriggerTimes, isTestx0021x105E, isAddNamePostFixes, isSaveNativeEndian, isOneDirAtATime, isRenameNotConvert, isSave3D, isGz, isPipedGz, isFlipY, isCreateBIDS, isSortDTIbyBVal, isAnonymizeBIDS, isOnlyBIDS, isCreateText, isForceOnsetTimes, isIgnoreDerivedAnd2D, isPhilipsFloatNotDisplayScaling, isIgnoreIntensityScaling, isTiltCorrect, isRGBplanar, isOnlySingleFile, isForceStackDCE, isIgnoreSeriesInstanceUID, isRotate3DAcq, isCrop, isGuessBidsFilename;
 	int saveFormat, isMaximize16BitRange, isForceStackSameSeries, nameConflictBehavior, isVerbose, isProgress, compressFlag, dirSearchDepth, onlySearchDirForDICOM, gzLevel, diffCyclingModeGE; // support for compressed data 0=none,
 	char filename[kOptsStr], outdir[kOptsStr], indir[kOptsStr], pigzname[kOptsStr], optsname[kOptsStr], indirParent[kOptsStr], imageComments[24], bidsSubject[kOptsStr], bidsSession[kOptsStr];
 	double seriesNumber[MAX_NUM_SERIES]; // requires double must store -1 (report but do not convert) as well as seriesUidCrc (uint32)