From 99f37fa1c021c4e30a719fff557e97fb568b3972 Mon Sep 17 00:00:00 2001
From: Chris Rorden <rorden@mailbox.sc.edu>
Date: Thu, 8 Nov 2018 19:06:17 -0500
Subject: [PATCH] Not all GE DWI with b>0 bvec=0 are trace
 (https://github.com/rordenlab/dcm2niix/issues/245)

---
 console/nii_dicom.cpp       |  4 ++--
 console/nii_dicom.h         |  2 +-
 console/nii_dicom_batch.cpp | 17 ++++++++++++++---
 3 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp
index 09c15a12..b37763ab 100644
--- a/console/nii_dicom.cpp
+++ b/console/nii_dicom.cpp
@@ -5868,7 +5868,7 @@ if (d.isHasPhase)
                 pow(d.patientPosition[2]-d.patientPositionLast[2],2)+
                 pow(d.patientPosition[3]-d.patientPositionLast[3],2));
             dx = dx / (maxInStackPositionNumber - 1);
-			if (dx > 0.0)
+			if ((dx > 0.0) && (!isSameFloatGE(dx, d.xyzMM[3])) ) //patientPosition has some rounding error
 				d.xyzMM[3] = dx;
 		} //d.zSpacing <= 0.0: Bruker does not populate 0018,0088 https://github.com/rordenlab/dcm2niix/issues/241
     } //if numDimensionIndexValues > 1 : enhanced DICOM
@@ -5935,7 +5935,7 @@ if (d.isHasPhase)
     #ifndef myLoadWholeFileToReadHeader
 	fclose(file);
 	#endif
-	//printf("%g\t\t%g\t%g\t%g\n", d.CSA.dtiV[0], d.CSA.dtiV[1], d.CSA.dtiV[2], d.CSA.dtiV[3]);
+	//printf("%g\t\t%g\t%g\t%g\t%s\n", d.CSA.dtiV[0], d.CSA.dtiV[1], d.CSA.dtiV[2], d.CSA.dtiV[3], fname);
 	//printMessage("buffer usage %d  %d  %d\n",d.imageStart, lPos+lFileOffset, MaxBufferSz);
 	return d;
 } // readDICOM()
diff --git a/console/nii_dicom.h b/console/nii_dicom.h
index 094d0732..678db596 100644
--- a/console/nii_dicom.h
+++ b/console/nii_dicom.h
@@ -43,7 +43,7 @@ extern "C" {
 	#define kCCsuf " CompilerNA" //unknown compiler!
 #endif
 
-#define kDCMvers "v1.0.20181107 " kJP2suf kLSsuf kCCsuf
+#define kDCMvers "v1.0.20181108 " kJP2suf kLSsuf kCCsuf
 
 static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic
 static const int kMaxDTI4D = 18000; //maximum number of DTI directions for 4D (Philips) images, also maximum number of 3D slices for Philips 3D and 4D images
diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp
index ed457faf..24f3fbab 100644
--- a/console/nii_dicom_batch.cpp
+++ b/console/nii_dicom_batch.cpp
@@ -233,8 +233,11 @@ void geCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx){
         	float bVal = vx[i].V[0] * (vLen * vLen);
         	printMessage("GE BVal scaled %g -> %g\n", vx[i].V[0], bVal);
         	vx[i].V[0] = bVal;
+        	vx[i].V[1] = vx[i].V[1]/vLen;
+        	vx[i].V[2] = vx[i].V[2]/vLen;
+        	vx[i].V[3] = vx[i].V[3]/vLen;
        	}
-        if (!col) { //rows need to be swizzled
+       	if (!col) { //rows need to be swizzled
         	//see Stanford dataset Ax_DWI_Tetrahedral_7 unable to resolve between possible solutions
         	// http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
             float swap = vx[i].V[1];
@@ -1316,18 +1319,26 @@ int * nii_SaveDTI(char pathoutname[],int nConvert, struct TDCMsort dcmSort[],str
 	float kADCval = maxB0 + 1; //mark as unusual
     *numADC = 0;
 	bvals = (float *) malloc(numDti * sizeof(float));
+	int numGEwarn = 0;
 	for (int i = 0; i < numDti; i++) {
 		bvals[i] = vx[i].V[0];
 		//printMessage("---bxyz %g %g %g %g\n",vx[i].V[0],vx[i].V[1],vx[i].V[2],vx[i].V[3]);
 		//Philips includes derived isotropic images
-		if (((dcmList[indx0].manufacturer == kMANUFACTURER_GE) || (dcmList[indx0].manufacturer == kMANUFACTURER_PHILIPS)) && (isADCnotDTI(vx[i]))) {
+		//if (((dcmList[indx0].manufacturer == kMANUFACTURER_GE) || (dcmList[indx0].manufacturer == kMANUFACTURER_PHILIPS)) && (isADCnotDTI(vx[i]))) {
+        if (((dcmList[indx0].manufacturer == kMANUFACTURER_GE)) && (isADCnotDTI(vx[i]))) {
+            numGEwarn += 1;
+            vx[i].V[0] = 0;
+        } //see issue 245
+        if (((dcmList[indx0].manufacturer == kMANUFACTURER_PHILIPS)) && (isADCnotDTI(vx[i]))) {
             *numADC = *numADC + 1;
             bvals[i] = kADCval;
             //printMessage("+++bxyz %d\n",i);
         }
         bvals[i] = bvals[i] + (0.5 * i/numDti); //add a small bias so ties are kept in sequential order
 	}
-	if (*numADC == numDti ) {
+	if (numGEwarn > 0)
+		printWarning("Some images had bval>0 but bvec=0 (either Trace or b=0, see issue 245)\n");
+	if ((*numADC == numDti) || (numGEwarn  == numDti)) {
 		//all isotropic/ADC images - no valid bvecs
 		*numADC = 0;
 		free(bvals);