Merge pull request #11 from mslw/new-suffix

Enable field maps from AP & PA EPI
mslw · May 11, 2022 · a0ee265 · a0ee265
2 parents 75f8b77 + fcc6778
commit a0ee265
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project versioning is based on [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [1.0.1] - 2022-05-11
+### Added
+- Enabled blip-up & blip-down fieldmap EPI (dir-AP_epi & dir-PA_epi)
+- Internal: added dir to OBOSeries
+
 ## [1.0.0] - 2018-08-10
 ### Added
 - Optional scans.tsv file (containing relative path, scan date and time for all scans within a subject/session) can be optionally created

diff --git a/GeneralMappingWindow.xib b/GeneralMappingWindow.xib
@@ -93,6 +93,8 @@
                                                                     <string>T1w</string>
                                                                     <string>bold</string>
                                                                     <string>(fmap)</string>
+                                                                    <string>dir-AP_epi</string>
+                                                                    <string>dir-PA_epi</string>
                                                                     <string>dwi</string>
                                                                     <string>T2w</string>
                                                                     <string>T1map</string>

diff --git a/GeneralMappingWindowController.m b/GeneralMappingWindowController.m
@@ -215,6 +215,12 @@ -(void) annotateAllSeries {
             OBOSeries *decoratedSeries = [[OBOSeries alloc] initWithSeries:currentSeries params:[sharedData.seriesDescription objectForKey:currentSeries.name]];
             [decoratedSeries setValue:subjectName forKey:@"participant"];
             [decoratedSeries setValue:sessionLabel forKey:@"session"];
+	    if ([[decoratedSeries suffix] hasSuffix:@"_epi"]){
+	        // our GUI allows dir-AP_epi and dir-PA_epi "suffixes", translate them into dir & suffix
+	        [decoratedSeries setValue:[self getDirFromSuffix:[decoratedSeries suffix]] forKey:@"dir"];
+	        [decoratedSeries setValue:@"epi" forKey:@"suffix"];
+	    }
+
             [decoratedFromCurrentStudy addObject:decoratedSeries];
             [namesFromCurrentStudy addObject:currentSeries.name];
         }
@@ -421,6 +427,18 @@ -(NSString*) createSubjectNameForStudy:(DicomStudy *)study {
 
 }
 
+-(NSString*) getDirFromSuffix:(NSString *)suffix {
+  // little helper for getting dir label from "dir-(AP|PA)_epi"
+  NSString *result = @"";
+  if ([suffix hasPrefix:@"dir-AP"]) {
+    result = @"AP";
+  }
+  else if ([suffix hasPrefix:@"dir-PA"]) {
+    result = @"PA";
+  }
+  return result;
+}
+
 -(void) createDatasetDescription {
     OBOCollectedData *sharedData = [OBOCollectedData sharedManager];
     [sharedData.datasetDescription removeAllObjects];

diff --git a/HorosBidsOutput-Info.plist b/HorosBidsOutput-Info.plist
@@ -13,11 +13,11 @@
 	<key>CFBundlePackageType</key>
 	<string>BNDL</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.0.0</string>
+	<string>1.1.0</string>
 	<key>CFBundleSignature</key>
 	<string>????</string>
 	<key>CFBundleVersion</key>
-	<string>1.0.0</string>
+	<string>1.1.0</string>
 	<key>MenuTitles</key>
 	<array>
 		<string>BIDS output</string>

diff --git a/Info.plist b/Info.plist
@@ -16,12 +16,12 @@
 	<string>????</string>
 	<key>CFBundleVersion</key>
 	<string>1.0</string>
-	<key>NSPrincipalClass</key>
-	<string>BidsOutputFilter</string>
 	<key>MenuTitles</key>
 	<array>
 		<string>BIDS output</string>
 	</array>
+	<key>NSPrincipalClass</key>
+	<string>BidsOutputFilter</string>
 	<key>pluginType</key>
 	<string>Database</string>
 </dict>

diff --git a/OBOSeries.h b/OBOSeries.h
@@ -34,6 +34,7 @@
 @property (nonatomic) NSString *session;
 @property (nonatomic) NSString *task;
 @property (nonatomic) NSString *acq;
+@property (nonatomic) NSString *dir;
 @property (nonatomic) NSString *run;
 
 @property (nonatomic, assign) BOOL discard;

diff --git a/OBOSeries.m b/OBOSeries.m
@@ -40,6 +40,7 @@ - (instancetype)init {
         _session = @"";
         _task = @"";
         _acq = @"";
+	_dir = @"";
         _run = @"";
 
         _discard = NO;
@@ -60,6 +61,7 @@ - (instancetype)initWithSeries:(DicomSeries *)originalSeries {
         _session = @"";
         _task = @"";
         _acq = @"";
+	_dir = @"";
         _run = @"";
 
         _discard = NO;
@@ -80,6 +82,8 @@ -(instancetype)initWithSeries:(DicomSeries *)originalSeries params:(NSDictionary
         _session = @""; // set after initialisation
         _task = [params valueForKey:@"task"];
         _acq = [params valueForKey:@"acq"];
+	_dir = @"";  // set after initialisation, currently just for for phase-encoding polarity field map
+	//[params valueForKey:@"dir"] ?: @""  // might be the syntax to get with default
         _run = [params valueForKey:@"run"];
 
         _discard = NO;
@@ -94,7 +98,7 @@ -(NSString*)getBidsPath {
     NSArray *anatSuffixList = @[@"T1w", @"T2w", @"T1rho", @"T1map", @"T2map", @"T2star", @"FLAIR", @"FLASH",
                                 @"PD", @"PDmap", @"PDT2", @"inplaneT1", @"inplaneT2", @"angio", @"defacemask",
                                 @"SWImagandphase"];
-    NSArray *fmapSuffixList = @[@"phasediff", @"magnitude1", @"magnitude2"];
+    NSArray *fmapSuffixList = @[@"phasediff", @"magnitude1", @"magnitude2", @"epi"];
     NSMutableString *path = [[NSMutableString alloc] init];
     if ([self discard]){
         return path;
@@ -221,6 +225,13 @@ -(NSString*)getBidsPath {
             [path appendString:@"_acq-"];
             [path appendString:self.acq];
         }
+
+	// dir (required for PEpolar field map)
+	if ([self.suffix isEqualToString:@"epi"]) {
+	  // ADD ce (optional) - not yet supported
+	  [path appendString:@"_dir-"];
+	  [path appendString:self.dir];
+	}
 
         // run (optional)
         if ([self.run length] > 0){

diff --git a/OsirixBidsOutput.xcodeproj/project.pbxproj b/OsirixBidsOutput.xcodeproj/project.pbxproj
@@ -59,7 +59,7 @@
 
 /* Begin PBXFileReference section */
 		089C1672FE841209C02AAC07 /* Foundation.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = Foundation.framework; path = /System/Library/Frameworks/Foundation.framework; sourceTree = "<absolute>"; };
-		089C167EFE841241C02AAC07 /* English */ = {isa = PBXFileReference; fileEncoding = 10; lastKnownFileType = text.plist.strings; name = English; path = English.lproj/InfoPlist.strings; sourceTree = "<group>"; };
+		089C167EFE841241C02AAC07 /* English */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.plist.strings; name = English; path = English.lproj/InfoPlist.strings; sourceTree = "<group>"; };
 		089C167FFE841241C02AAC07 /* AppKit.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = AppKit.framework; path = /System/Library/Frameworks/AppKit.framework; sourceTree = "<absolute>"; };
 		1058C7ADFEA557BF11CA2CBB /* Cocoa.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = Cocoa.framework; path = /System/Library/Frameworks/Cocoa.framework; sourceTree = "<absolute>"; };
 		8420023112E829A200E1E9CE /* OsiriXAPI.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; path = OsiriXAPI.framework; sourceTree = "<group>"; };