Apply voxel intensity scaling to .nii loaded untouched

NiftiMod is using load_untouch_nii for some time leavign the data untransformed. However the voxel intensities should be scaled

Author: adhusch

lib/NiftiOOP/NiftiMod.m

@@ -85,8 +85,10 @@
         function [image, header] = load(this)
             if( ~this.isLoaded && ~strcmp(this.filepath,'')) % it is not already isLoaded and we were not called with empty string (by Matlab callingn our get functions without command after initiating!)
                 disp(['Loading ' this.filepath ' from disk...']);
-                % nifti = load_nii(this.filepath, [], [], [], [], [], 0.1, 'q'); % load with 0.1 tolerance, prefer the q-form over the sform!
-                nifti = load_untouch_nii(this.filepath); % load with 0.1 tolerance, prefer the q-form over the sform!
+                %nifti = load_nii(this.filepath, [], [], [], [], [], 0.1, 'q'); % load with 0.1 tolerance, prefer the q-form over the sform!
+                nifti = load_untouch_nii(this.filepath); % load untouched, i.e. keep orginial data orientation (dont apply any transform)
+                nifti = applyNiiIntensityScaling(nifti); %however, the voxel intesities should be scaled correctly now here (as they
+%would by load_nii otherewise)
 
                 this.header  = nifti.hdr; % header should maybe kept all the time ..
 

lib/NiftiOOP/applyNiiIntensityScaling.m

@@ -0,0 +1,61 @@
+function nii = applyNiiIntensityScaling(nii)
+% Code extracte from Jimmy Shen's (jimmy@rotman-baycrest.on.ca) xform_nii.m
+% method, which is part of the nifti toolbox
+%
+% Andreas Husch, 2019
+
+    %  if scl_slope field is nonzero, then each voxel value in the
+       %  dataset should be scaled as: y = scl_slope * x + scl_inter
+       %  I bring it here because hdr will be modified by change_hdr.
+       %
+       if nii.hdr.dime.scl_slope ~= 0 & ...
+        ismember(nii.hdr.dime.datatype, [2,4,8,16,64,256,512,768]) & ...
+        (nii.hdr.dime.scl_slope ~= 1 | nii.hdr.dime.scl_inter ~= 0)
+
+          nii.img = ...
+        nii.hdr.dime.scl_slope * double(nii.img) + nii.hdr.dime.scl_inter;
+
+          if nii.hdr.dime.datatype == 64
+
+             nii.hdr.dime.datatype = 64;
+             nii.hdr.dime.bitpix = 64;
+          else
+             nii.img = single(nii.img);
+
+             nii.hdr.dime.datatype = 16;
+             nii.hdr.dime.bitpix = 32;
+          end
+
+          nii.hdr.dime.glmax = max(double(nii.img(:)));
+          nii.hdr.dime.glmin = min(double(nii.img(:)));
+
+          %  set scale to non-use, because it is applied in xform_nii
+          %
+          nii.hdr.dime.scl_slope = 0;
+
+       end
+
+       %  However, the scaling is to be ignored if datatype is DT_RGB24.
+
+       %  If datatype is a complex type, then the scaling is to be applied
+       %  to both the real and imaginary parts.
+       %
+       if nii.hdr.dime.scl_slope ~= 0 & ...
+        ismember(nii.hdr.dime.datatype, [32,1792])
+
+          nii.img = ...
+        nii.hdr.dime.scl_slope * double(nii.img) + nii.hdr.dime.scl_inter;
+
+          if nii.hdr.dime.datatype == 32
+             nii.img = single(nii.img);
+          end
+
+          nii.hdr.dime.glmax = max(double(nii.img(:)));
+          nii.hdr.dime.glmin = min(double(nii.img(:)));
+
+          %  set scale to non-use, because it is applied in xform_nii
+          %
+          nii.hdr.dime.scl_slope = 0;
+
+       end
+end