Update dcm_qa_nih submodule.

README.md

@@ -74,16 +74,15 @@ If you have any problems with the cmake build script described above or want to
 
 ## Alternatives
 
- - [Valerio Luccio's dinifti](http://cbi.nyu.edu/software/dinifti.php) is focused on conversion of Siemens data.
+ - [dinifti](http://cbi.nyu.edu/software/dinifti.php) is focused on conversion of Siemens data.
  - [dcm2nii](http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.htm) is the predecessor of dcm2niix. It is deprecated for modern images, but does handle image formats that predate DICOM (proprietary Elscint, GE and Siemens formats).
  - [DWIConvert](https://github.com/BRAINSia/BRAINSTools/tree/master/DWIConvert) converts DICOM images to NRRD and NIfTI formats.
- - [Xiangrui Li's dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter) is written in Matlab. The Matlab language makes this very scriptable.
+ - [dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter) is written in Matlab. The Matlab language makes this very scriptable.
  - [dicom2nifti](https://github.com/icometrix/dicom2nifti) uses the scriptable Python wrapper utilizes the [high performance  GDCMCONV](http://gdcm.sourceforge.net/wiki/index.php/Gdcmconv) executables.
  - [MRtrix mrconvert](http://mrtrix.readthedocs.io/en/latest/reference/commands/mrconvert.html) is a useful general purpose image converter and handles DTI data well. It is an outstanding tool for modern Philips enhanced images.
- - [Jolinda Smith's mcverter](http://lcni.uoregon.edu/%7Ejolinda/MRIConvert/) has great support for various vendors.
+ - [mcverter](http://lcni.uoregon.edu/%7Ejolinda/MRIConvert/) has great support for various vendors.
  - [mri_convert](https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html) is part of the popular FreeSurfer package. In my limited experience this tool works well for GE and Siemens data, but fails with Philips 4D datasets.
  - [SPM12](http://www.fil.ion.ucl.ac.uk/spm/software/spm12/) is one of the most popular tools in the field. It includes DICOM to NIfTI conversion. Being based on Matlab it is easy to script.
- - [R2A_GUI](http://r2agui.sourceforge.net/) is a Matlab script that converts Philips PAR/REC images to NIfTI.
 
 ## Links
 

console/nii_dicom.cpp

@@ -819,6 +819,26 @@ struct TDICOMdata clear_dicom_data() {
     return d;
 } //clear_dicom_data()
 
+int isdigitdot(int c) { //returns true if digit or '.'
+	if (c == '.') return 1;
+	return isdigit(c);
+}
+
+void dcmStrDigitsDotOnlyKey(char key, char* lStr) {
+    //e.g. string "F:2.50" returns 2.50 if key==":"
+    size_t len = strlen(lStr);
+    if (len < 1) return;
+    bool isKey = false;
+    for (int i = 0; i < (int) len; i++) {
+        if (!isdigitdot(lStr[i]) ) {
+            isKey =  (lStr[i] == key);
+            lStr[i] = ' ';
+
+        } else if (!isKey)
+        	lStr[i] = ' ';
+    }
+} //dcmStrDigitsOnlyKey()
+
 void dcmStrDigitsOnlyKey(char key, char* lStr) {
     //e.g. string "p2s3" returns 2 if key=="p" and 3 if key=="s"
     size_t len = strlen(lStr);
@@ -3966,6 +3986,7 @@ const uint32_t kEffectiveTE  = 0x0018+ (0x9082 << 16);
 #define  kPETImageIndex  0x0054+(0x1330<< 16 )
 #define  kPEDirectionDisplayedUIH  0x0065+(0x1005<< 16 )//SH
 #define  kDiffusion_bValueUIH  0x0065+(0x1009<< 16 ) //FD
+#define  kParallelInformationUIH  0x0065+(0x100D<< 16 ) //SH
 #define  kNumberOfImagesInGridUIH  0x0065+(0x1050<< 16 ) //DS
 #define  kMRVFrameSequenceUIH  0x0065+(0x1050<< 16 ) //SQ
 #define  kDiffusionGradientDirectionUIH  0x0065+(0x1037<< 16 ) //FD
@@ -4889,6 +4910,14 @@ double TE = 0.0; //most recent echo time recorded
             	d.CSA.numDti = 1;
             	//printf("%d>>>%g\n", lPos, v[0]);
             	break; }
+            case kParallelInformationUIH: {//SENSE factor (0065,100d) SH [F:2S]
+            	if (d.manufacturer != kMANUFACTURER_UIH) break;
+            	char accelStr[kDICOMStr];
+                dcmStr (lLength, &buffer[lPos], accelStr);
+                char *ptr;
+                dcmStrDigitsDotOnlyKey(':', accelStr); //e.g. if "p2s4" return "2", if "s4" return ""
+				d.accelFactPE = atof(accelStr);
+                break; }
             case kNumberOfImagesInGridUIH :
             	if (d.manufacturer != kMANUFACTURER_UIH) break;
             	d.numberOfImagesInGridUIH =  dcmStrFloat(lLength, &buffer[lPos]);

console/nii_dicom_batch.cpp

@@ -980,15 +980,16 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
 		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.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)
-				pf = (float)pf / (float)d.accelFactPE; //estimate: not sure if we round up or down
-			pf = (float)d.echoTrainLength / (float)pf;
-			if (pf < 1.0) //e.g. if difference between lines and echo length not all explained by iPAT (SENSE/GRAPPA)
-				fprintf(fp, "\t\"PartialFourier\": %g,\n", pf);
+		if ((!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)
+					pf = (float)pf / (float)d.accelFactPE; //estimate: not sure if we round up or down
+				pf = (float)d.echoTrainLength / (float)pf;
+				if (pf < 1.0) //e.g. if difference between lines and echo length not all explained by iPAT (SENSE/GRAPPA)
+					fprintf(fp, "\t\"PartialFourier\": %g,\n", pf);
 		} //compute partial Fourier: not reported in XA10, so infer
+		//printf("PhaseLines=%d EchoTrainLength=%d  SENSE=%g\n", d.phaseEncodingLines, d.echoTrainLength, d.accelFactPE); //n.b. we can not distinguish pF from SENSE/GRAPPA for UIH
 	}
 	#endif
 	if (d.CSA.multiBandFactor > 1) //AccelFactorSlice
@@ -1018,7 +1019,7 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
     if (bandwidthPerPixelPhaseEncode == 0.0)
     	bandwidthPerPixelPhaseEncode = 	d.CSA.bandwidthPerPixelPhaseEncode;
     json_Float(fp, "\t\"BandwidthPerPixelPhaseEncode\": %g,\n", bandwidthPerPixelPhaseEncode );
-    if (d.accelFactPE > 1.0) fprintf(fp, "\t\"ParallelReductionFactorInPlane\": %g,\n", d.accelFactPE);
+    if ((!d.is3DAcq) && (d.accelFactPE > 1.0)) fprintf(fp, "\t\"ParallelReductionFactorInPlane\": %g,\n", d.accelFactPE);
 	//EffectiveEchoSpacing
 	// Siemens bandwidthPerPixelPhaseEncode already accounts for the effects of parallel imaging,
 	// interpolation, phaseOversampling, and phaseResolution, in the context of the size of the