From 6c5f177ad97daf2b7b34ae0a3f08839a08c87dd3 Mon Sep 17 00:00:00 2001
From: neurolabusc <rorden@sc.edu>
Date: Thu, 7 Sep 2023 05:52:26 -0700
Subject: [PATCH] improve bids guess
 (https://github.com/rordenlab/dcm2niix/issues/751)

---
 console/nii_dicom.cpp       |  4 ++++
 console/nii_dicom_batch.cpp | 19 +++++++++++++------
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp
index 0cf25ee6..37104fe1 100644
--- a/console/nii_dicom.cpp
+++ b/console/nii_dicom.cpp
@@ -7921,6 +7921,8 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 	//if (contentTime != 0.0) && (numDimensionIndexValues < (MAX_NUMBER_OF_DIMENSIONS - 1)){
 	//	uint_32t timeCRC = mz_crc32X((unsigned char*) &contentTime, sizeof(double));
 	//}
+	if (numberOfFramesICEdims < 2) //issue751: icedims[20] frames for EPI only
+		numberOfFramesICEdims = 0;
 	if ((numberOfFramesICEdims > 0) && (d.xyzDim[3] != numberOfFramesICEdims)) {
 		printWarning("Series %ld includes partial volume (issue 742): %d slices acquired but ICE dims (0021,118e) specifies %d \n", d.seriesNum, d.xyzDim[3], numberOfFramesICEdims);
 		d.seriesNum += 1000;
@@ -8136,6 +8138,8 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 		d.isValid = false;
 	}
 	//printf("%g\t%g\t%s\n", d.intenIntercept, d.intenScale, fname);
+	if ((d.isLocalizer) && (strstr(d.seriesDescription, "b1map"))) //issue751 b1map uses same base as scout
+			d.isLocalizer = false;
 	return d;
 } // readDICOMx()
 
diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp
index afe6102d..5dd0f8d9 100644
--- a/console/nii_dicom_batch.cpp
+++ b/console/nii_dicom_batch.cpp
@@ -6442,12 +6442,10 @@ void reportProtocolBlockGE(struct TDICOMdata *d, const char *filename, int isVer
 #endif
 } //bidsGE
 
-void bidsStr() { //
-
-}
-
 void setBidsSiemens(struct TDICOMdata *d, int nConvert, int isVerbose, const char *filename) {
 	char seqDetails[kDICOMStrLarge] = "";
+	char acqStr[kDICOMStrLarge] = "";
+	char preAcqStr[kDICOMStrLarge] = "";
 	float inv1 = NAN;
 	float inv2 = NAN;
 	bool isDualTI = false;
@@ -6499,6 +6497,15 @@ void setBidsSiemens(struct TDICOMdata *d, int nConvert, int isVerbose, const cha
 	if (((d->xyzDim[3] < 2) && (nConvert < 1)) || (d->isLocalizer)) { //need nConvert or nifti header
 		strcpy(dataTypeBIDS, "discard");
 		strcpy(modalityBIDS, "localizer");
+	} else if (strstr(seqDetails,"b1map")) {
+		//issue 751 nb both T1 and b1map can use tfl base
+		//https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html#tb1tfl-and-tb1rfm-specific-notes
+		strcpy(dataTypeBIDS, "fmap");
+		strcpy(modalityBIDS, "TB1TFL");
+		if ((strstr(d->imageType, "FLIP ANGLE MAP")) || (strstr(d->imageType, "FLIP ANGLE MAP")))
+			strcpy(preAcqStr, "famp");
+		else
+			strcpy(preAcqStr, "anat");
 	} else if ((strstr(seqDetails, "tfl") != NULL) || (strstr(seqDetails, "mp2rage") != NULL) || (strstr(seqDetails, "wip925") != NULL)) { //prog_mprage
 		strcpy(dataTypeBIDS, "anat");
 		if (isDualTI)
@@ -6615,8 +6622,8 @@ void setBidsSiemens(struct TDICOMdata *d, int nConvert, int isVerbose, const cha
 		strcpy(modalityBIDS, "epi");
 		isDirLabel = true;
 	}
-	char acqStr[kDICOMStrLarge] = "";
-	strcat(acqStr, "_acq-");
+	strcpy(acqStr, "_acq-");
+	strcat(acqStr, preAcqStr);
 	int len = strlen(seqName);
 	if (len > 0) {
 		for (int i = 0; i < len; i++) {