Merge pull request #54 from kschan0214/dev1.2.2

Dev1.2.2

README.md

@@ -41,7 +41,12 @@ If you have a more general question regarding the usage of SEPIA and/or other QS
 
 For full update log, please visit https://sepia-documentation.readthedocs.io/en/latest/getting_started/Release-note.html.
 
-### 1.2.1.1 (current master)
+### 1.2.2 (current master)
+* Fix bug for non-double type input for MATLAB's strel function
+* Make sure all holes inside the ROI mask are filled after the background field removal step
+* ROI (brain) mask is applied on the fieldmap regardless of what method is chosen
+
+### 1.2.1.1 (current 941cd5b)
 * Enable option of GPU processing for FANSI and NDI
 
 ### 1.2.1 (current 190dd44)

sepia_universal_variables.m

@@ -14,7 +14,7 @@
 % DO NOT change the order of the entities, add a new one at the end instead
 %
 %% Version
-SEPIA_version = 'v1.2.1.1';
+SEPIA_version = 'v1.2.2';
 
 %% PATH
 SEPIA_HOME = fileparts(mfilename('fullpath'));

utils/refine_brain_mask_using_r2s.m

@@ -48,12 +48,12 @@
 open_radius_voxel   = min(round(open_radius_mm ./ voxelSize));
 close_radius_voxel  = min(round(close_radius_mm ./ voxelSize));
 
-% remove disconnected voxels
-mask_r2s_morph = imopen(mask_r2s, strel('sphere', open_radius_voxel));
+% remove disconnected voxels, 20230124 v1.2.2: second input of strel has to be double
+mask_r2s_morph = imopen(mask_r2s, strel('sphere', double(open_radius_voxel)));
 % get the largest single object
 mask_r2s_morph = getLargestObject(mask_r2s_morph);
-% reconnect voxels
-mask_r2s_morph = imclose(mask_r2s_morph, strel('sphere', close_radius_voxel));
+% reconnect voxels, 20230124 v1.2.2: second input of strel has to be double
+mask_r2s_morph = imclose(mask_r2s_morph, strel('sphere', double(close_radius_voxel)));
 % make sure no holes in the centre of the brain
 mask_r2s_morph = imfill(mask_r2s_morph,'holes');
 

wrapper/BackgroundRemovalMacroIOWrapper.m

@@ -123,7 +123,9 @@
 clear totalField maskLocalfield % clear variables that no longer be needed
 
 % generate new mask based on backgroudn field removal result
-mask_QSM = localField ~= 0;
+% mask_QSM = localField ~=0;
+% 20230124 v1.2.2: make sure no holes inide ROIs
+mask_QSM = imfill(localField ~= 0, 'holes');
 
 % save results
 fprintf('Saving local field map...');

wrapper/SepiaIOWrapper.m

@@ -164,6 +164,9 @@
 % core of temporo-spatial phase unwrapping
 [totalField,fieldmapSD,fieldmapUnwrapAllEchoes,mask] = estimateTotalField(fieldMap,mask,matrixSize,voxelSize,algorParam,headerAndExtraData);
 
+% 20230124 v1.2.2: apply mask on derived map
+totalField = totalField .* double(mask);
+
 % save unwrapped phase if chosen
 if ~isempty(fieldmapUnwrapAllEchoes) && isSaveUnwrappedEcho
     % save the output                           
@@ -292,7 +295,9 @@
 clear totalField maskLocalfield % clear variables that no longer be needed
 
 % generate new mask based on backgroudn field removal result
-mask_QSM = localField ~=0;
+% mask_QSM = localField ~=0;
+% 20230124 v1.2.2: make sure no holes inide ROIs
+mask_QSM = imfill(localField ~= 0, 'holes');
 
 fprintf('Saving local field map...');
 save_nii_quick(outputNiftiTemplate,localField, outputFileList.localField);

wrapper/UnwrapPhaseMacroIOWrapper.m

@@ -168,6 +168,9 @@
 % core of temporo-spatial phase unwrapping
 [totalField,fieldmapSD,fieldmapUnwrapAllEchoes,mask] = estimateTotalField(fieldMap,mask,matrixSize,voxelSize,algorParam,headerAndExtraData);
 
+% 20230124 v1.2.2: apply mask on derived map
+totalField = totalField .* double(mask);
+
 % save unwrapped phase if chosen
 if ~isempty(fieldmapUnwrapAllEchoes) && isSaveUnwrappedEcho
     % save the output