change MoCo naming and derived detection (#243)

FILENAMING.md

@@ -40,6 +40,7 @@ In general dcm2niix creates images with 3D dimensions, or 4 dimensions when the
  - _ADC Philips specific case. A DWI image where derived isotropic, ADC or trace volume was appended to the series. Since this image will disrupt subsequent processing, and because subsequent processing (dwidenoise, topup, eddy) will yield better derived images, dcm2niix will also create an additional image without this volume. Therefore, the _ADC file should typically be discarded. If you want dcm2niix to discard these useless derived images, use the ignore feature ('-i y').
  - _Eq is specific to [CT scans](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Computed_Tomography_.28CT.2C_CAT.29). These scans can be acquired with variable distance between the slices of a 3D volume. NIfTI asumes all 2D slices that form a 3D stack are equidistant. Therefore, dcm2niix reslices the input data to generate an equidistant volume.
  - _Tilt is specific to [CT scans](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Computed_Tomography_.28CT.2C_CAT.29). These scans can be acquired with a gantry tilt that causes a skew that can not be stored in a NIfTI qForm. Therefore, the slices are resampled to remove the effect of tilt.
+ - _MoCo is appended to the ProtocolName if Image Type (0008,0008) includes the term 'MOCO'. This helps disambiguate Siemens fMRI runs where both motion corrected and raw data is stored for a single session.
 
 ## Special Characters
 

console/nii_dicom.cpp

@@ -4066,6 +4066,7 @@ double TE = 0.0; //most recent echo time recorded
     int encapsulatedDataImageStart = 0; //position of 7FE0,0010 for compressed images (where actual image start should be start of first fragment)
     bool isOrient = false;
     bool isDcm4Che = false;
+    bool isMoCo = false;
     bool isIconImageSequence = false;
     bool isSwitchToImplicitVR = false;
     bool isSwitchToBigEndian = false;
@@ -4471,6 +4472,18 @@ double TE = 0.0; //most recent echo time recorded
             	dcmStr (lLength, &buffer[lPos], d.imageType);
                 int slen;
                 slen = (int) strlen(d.imageType);
+				if((slen > 5) && strstr(d.imageType, "_MOCO_") ) {
+                	//d.isDerived = true; //this would have 'i- y' skip MoCo images
+                	isMoCo = true;
+                }
+				if((slen > 5) && strstr(d.imageType, "_ADC_") )
+                	d.isDerived = true;
+				if((slen > 5) && strstr(d.imageType, "_TRACEW_") )
+                	d.isDerived = true;
+				if((slen > 5) && strstr(d.imageType, "_TRACE_") )
+                	d.isDerived = true;
+				if((slen > 5) && strstr(d.imageType, "_FA_") )
+                	d.isDerived = true;
 				//if (strcmp(transferSyntax, "ORIGINAL_PRIMARY_M_ND_MOSAIC") == 0)
                 if((slen > 5) && !strcmp(d.imageType + slen - 6, "MOSAIC") )
                 	isMosaic = true;
@@ -5707,6 +5720,8 @@ double TE = 0.0; //most recent echo time recorded
 		strcpy(d.protocolName, d.seriesDescription);
     if ((strlen(d.protocolName) < 1) && (strlen(d.seriesDescription) > 1))
 		strcpy(d.protocolName, d.seriesDescription);
+	if ((strlen(d.protocolName) > 1) && (isMoCo))
+		strcat (d.protocolName,"_MoCo"); //disambiguate MoCo https://github.com/neurolabusc/MRIcroGL/issues/31
     if ((strlen(d.protocolName) < 1) && (strlen(d.sequenceName) > 1) && (d.manufacturer != kMANUFACTURER_SIEMENS))
 		strcpy(d.protocolName, d.sequenceName); //protocolName (0018,1030) optional, sequence name (0018,0024) is not a good substitute for Siemens as it can vary per volume: *ep_b0 *ep_b1000#1, *ep_b1000#2, etc https://www.nitrc.org/forum/forum.php?thread_id=8771&forum_id=4703
 	//     if (!isOrient) {

console/nii_dicom.h

@@ -43,7 +43,7 @@ extern "C" {
 	#define kCCsuf " CompilerNA" //unknown compiler!
 #endif
 
-#define kDCMvers "v1.0.20181027 " kJP2suf kLSsuf kCCsuf
+#define kDCMvers "v1.0.20181030 " 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