fix bug when using BIDS compartible directory input, loading the magn…

…itude images does not take the rescale slope and intercept into account

README.md

@@ -41,7 +41,10 @@ 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.
 
-### 1.2.2.1 (current master)
+### 1.2.2.2 (current master)
+* Fix bug when using BIDS compatible directory input where magnitude images did not utilise the rescale slope and intercept to obtain the true values
+
+### 1.2.2.1 (current 1f04298)
 * Fix bug when using optimum weight total field computation with odd matrix size data
 
 ### 1.2.2 (current d6bb60e)

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 = 'v1.2.2.1';
+SEPIA_version = 'v1.2.2.2';
 
 %% PATH
 SEPIA_HOME = fileparts(mfilename('fullpath'));

utils/read_bids_to_filelist.m

@@ -15,7 +15,7 @@
 % Kwok-shing Chan @ DCCN
 % [email protected]
 % Date created: 11 August 2021 (v1.0)
-% Date modified:
+% Date modified: 9 February 2023 (v1.2.2.2)
 %
 %
 function inputNIFTIList = read_bids_to_filelist(inputDir,outputPrefix)
@@ -182,7 +182,9 @@ function save_nifti_as_4d(fileList, outputFilename, isPhase)
             if (abs(max(nii.img(:))-pi)>1e-4 || abs(min(nii.img(:))-(-pi))>1e-4) && isPhase % allow small differences possibly due to data stype conversion
                 img	= cat(4, img, DICOM2Phase(nii));
             else
-                img = cat(4, img, nii.img);
+%                 img = cat(4, img, nii.img);
+                % 20230209: bug fix applying rescale slope and intercept
+                img = cat(4, img, load_nii_img_only(fileList(k).name));
             end
 
             numFileLoaded = numFileLoaded + 1;