detect Siemens Phase maps

README.md

@@ -4,36 +4,40 @@ dcm2niix is a designed to convert neuroimaging data from the DICOM format to the
 
 ## Versions
 
+22-Apr-2016
+ - Detect Siemens Phase maps (phase image names end with "_ph").
+ - Use current working directory if file name not specified.
+
 12-Apr-2016
  - Provide override (command line option "-m y") to stack images of the same series even if they differ in study date/time, echo/coil number, or slice orientation. This mechanism allows users to concatenate images that break strict DICOM compliance.
 
 22-Mar-2016
  - Experimental support for [http://dicom.nema.org/dicom/2013/output/chtml/part10/chapter_7.html DICOM dataset's without DICOM file meta information].
 
 12-Dec-2015
- - Support PAR/REC FP values when possible(see PMC3998685)
+ - Support PAR/REC FP values when possible(see PMC3998685).
 
 11-Nov-2015
- - Minor refinements
+ - Minor refinements.
 
 12-June-2015
- - Uses less memory (helpful for large datasets)
+ - Uses less memory (helpful for large datasets).
 
 2-Feb-2015
- - Support for Visual Studio
- - Remove dependency on zlib (now uses miniz)
+ - Support for Visual Studio.
+ - Remove dependency on zlib (now uses miniz).
 
 1-Jan-2015
- - Images separated based on TE (fieldmaps)
- - Support for JPEG2000 using OpenJPEG or Jasper libraries
- - Support for JPEG using NanoJPEG library
- - Support for lossless JPEG using custom library
+ - Images separated based on TE (fieldmaps).
+ - Support for JPEG2000 using OpenJPEG or Jasper libraries.
+ - Support for JPEG using NanoJPEG library.
+ - Support for lossless JPEG using custom library.
 
 24-Nov-2014
- - Support for CT scans with gantry tilt and varying distance between slices
+ - Support for CT scans with gantry tilt and varying distance between slices.
 
 11-Oct-2014
- - Initial public release
+ - Initial public release.
 
 ## Running
 

console/nii_dicom.cpp

@@ -676,6 +676,8 @@ struct TDICOMdata clear_dicom_data() {
     d.CSA.slice_end = 0;
     d.CSA.protocolSliceNumber1 = 0;
     d.CSA.phaseEncodingDirectionPositive = -1; //unknown
+    d.CSA.isPhaseMap = false;
+    d.CSA.multiBandFactor = 1;
     return d;
 } //clear_dicom_data()
 
@@ -909,6 +911,33 @@ float csaMultiFloat (unsigned char buff[], int nItems, float Floats[], int *Item
     return Floats[1];
 } //csaMultiFloat()
 
+bool csaIsPhaseMap (unsigned char buff[], int nItems) {
+    //returns true if the tag "ImageHistory" has an item named "CC:ComplexAdd"
+    TCSAitem itemCSA;
+    if (nItems < 1)  return false;
+    int lPos = 0;
+    for (int lI = 1; lI <= nItems; lI++) {
+        memcpy(&itemCSA, &buff[lPos], sizeof(itemCSA));
+        lPos +=sizeof(itemCSA);
+        if (itemCSA.xx2_Len > 0) {
+#ifdef _MSC_VER
+            char * cString = (char *)malloc(sizeof(char) * (itemCSA.xx2_Len));
+#else
+            char cString[itemCSA.xx2_Len];
+#endif
+            memcpy(cString, &buff[lPos], sizeof(cString)); //TPX memcpy(&cString, &buff[lPos], sizeof(cString));
+            lPos += ((itemCSA.xx2_Len +3)/4)*4;
+            //printf(" %d item length %d = %s\n",lI, itemCSA.xx2_Len, cString);
+            if (strcmp(cString, "CC:ComplexAdd") == 0)
+                return true;
+#ifdef _MSC_VER
+            free(cString);
+#endif
+        }
+    } //for each item
+    return false;
+} //csaIsPhaseMap()
+
 int readCSAImageHeader(unsigned char *buff, int lLength, struct TCSAdata *CSA, int isVerbose, struct TDTI4D *dti4D) {
     //see also http://afni.nimh.nih.gov/pub/dist/src/siemens_dicom_csa.c
     //printf("%c%c%c%c\n",buff[0],buff[1],buff[2],buff[3]);
@@ -925,9 +954,12 @@ int readCSAImageHeader(unsigned char *buff, int lLength, struct TCSAdata *CSA, i
     for (int lT = 1; lT <= lnTag; lT++) {
         memcpy(&tagCSA, &buff[lPos], sizeof(tagCSA)); //read tag
         lPos +=sizeof(tagCSA);
-        //printf("%d CSA of %s %d\n",lPos, tagCSA.name, tagCSA.nitems);
+        if (isVerbose > 1) //extreme verbosity: show every CSA tag
+        	printf("%d CSA of %s %d\n",lPos, tagCSA.name, tagCSA.nitems);
         if (tagCSA.nitems > 0) {
-            if (strcmp(tagCSA.name, "NumberOfImagesInMosaic") == 0)
+            if (strcmp(tagCSA.name, "ImageHistory") == 0)
+                CSA->isPhaseMap =  csaIsPhaseMap(&buff[lPos], tagCSA.nitems);
+            else if (strcmp(tagCSA.name, "NumberOfImagesInMosaic") == 0)
                 CSA->mosaicSlices = (int) round(csaMultiFloat (&buff[lPos], 1,lFloats, &itemsOK));
             else if (strcmp(tagCSA.name, "B_value") == 0) {
                 CSA->dtiV[0] = csaMultiFloat (&buff[lPos], 1,lFloats, &itemsOK);
@@ -2840,6 +2872,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
                 break;
             case 	kCSAImageHeaderInfo:
                 readCSAImageHeader(&buffer[lPos], lLength, &d.CSA, isVerbose, dti4D);
+                d.isHasPhase = d.CSA.isPhaseMap;
                 break;
                 //case kObjectGraphics:
                 //    printf("---->%d,",lLength);

console/nii_dicom.h

@@ -11,12 +11,12 @@ extern "C" {
 #endif
 
 #ifdef myEnableJasper
-    #define kDCMvers "12Apr2016j" //JASPER for JPEG2000
+    #define kDCMvers "22Apr2016j" //JASPER for JPEG2000
 #else
 	#ifdef myDisableOpenJPEG
-    #define kDCMvers "12Apr2016" //no decompressor
+    #define kDCMvers "22Apr2016" //no decompressor
 	#else
-    #define kDCMvers "12Apr2016o" //OPENJPEG for JPEG2000
+    #define kDCMvers "22Apr2016o" //OPENJPEG for JPEG2000
     #endif
 #endif
 
@@ -45,6 +45,7 @@ static const int kCompress50 = 3; //obsolete JPEG lossy
     };
 
     struct TCSAdata {
+    	bool isPhaseMap;
         float dtiV[4], sliceNormV[4], bandwidthPerPixelPhaseEncode, sliceMeasurementDuration;
         int numDti, multiBandFactor, sliceOrder, slice_start, slice_end, mosaicSlices,protocolSliceNumber1,phaseEncodingDirectionPositive;
     };

console/nii_dicom_batch.cpp

@@ -87,6 +87,7 @@ void dropFilenameFromPath(char *path) { //
         strcpy(path,"");
     } else
         path[dirPath - path] = 0; // please make sure there is enough space in TargetDirectory
+    if (strlen(path) == 0) strcat (path,"."); //relative path - use cwd
 }
 
 
@@ -715,14 +716,16 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt
         } //found a % character
         pos++;
     } //for each character in input
-    if (dcm.echoNum > 1) {
+    if (dcm.coilNum > 1) {
         sprintf(newstr, "_c%d", dcm.coilNum);
         strcat (outname,newstr);
     }
     if (dcm.echoNum > 1) {
-        sprintf(newstr, "_%d", dcm.echoNum);
+        sprintf(newstr, "_e%d", dcm.echoNum);
         strcat (outname,newstr);
     }
+    if (dcm.isHasPhase)
+    	strcat (outname,"_ph"); //manufacturer name not available
     if (pos > start) { //append any trailing characters
         strncpy(&newstr[0], &inname[0] + start, pos - start);
         newstr[pos - start] = '\0';
@@ -1413,8 +1416,12 @@ bool isSameSet (struct TDICOMdata d1, struct TDICOMdata d2, bool isForceStackSam
      printf("slices not stacked: Study Data/Time (0008,0020 / 0008,0030) varies %12.12f ~= %12.12f\n", d1.dateTime, d2.dateTime);
      return false;
     }
-    if ((d1.TE != d2.TE)  || (d1.coilNum != d2.coilNum)  ||  (d1.echoNum != d2.echoNum)) {
-        printf("filse not stacked: echo or coil varies\n");
+    if ((d1.TE != d2.TE) || (d1.echoNum != d2.echoNum)) {
+        printf("slices not stacked: echo varies (TE %g, %g; echo %d, %d)\n", d1.TE, d2.TE,d1.echoNum, d2.echoNum );
+        return false;
+    }
+    if (d1.coilNum != d2.coilNum) {
+        printf("slices not stacked: coil varies\n");
         return false;
     }
     if (strcmp(d1.protocolName, d2.protocolName) != 0) {
@@ -1790,7 +1797,6 @@ int nii_loadDir (struct TDCMopts* opts) {
         return convert_foreign(*opts);
     }*/
     getFileName(opts->indirParent, opts->indir);
-    //printf("XXXXXXX %s\n XXX\n", opts->indirParent); return EXIT_FAILURE;
     if (isFile && ((isExt(indir, ".par")) || (isExt(indir, ".rec"))) ) {
         char pname[512], rname[512];
         strcpy(pname,indir);