diff --git a/ext_libs/EasyReg/ea_easyreg.m b/ext_libs/EasyReg/ea_easyreg.m
index 8fec2cc69..caf2fdbdc 100644
--- a/ext_libs/EasyReg/ea_easyreg.m
+++ b/ext_libs/EasyReg/ea_easyreg.m
@@ -67,14 +67,14 @@
 
 function [] = freesurfer_nii_to_itk_h5(warp_file_in, warp_file_out)
 
-% substract mm coordinates for each voxel
-n = load_nii(warp_file_in);
+% Subtract millimeter coordinates for each voxel
+n = load_untouch_nii(warp_file_in);
 s = n.hdr.dime.dim(2:4);
 index = 1:prod(s);
 [v1,v2,v3] = ind2sub(s,index);
 mm = ea_vox2mm([v1',v2',v3'], ea_get_affine(warp_file_in)); % Need to do vox2mm since EasyReg uses disp_crs format)
 mm = reshape(mm, [s,3]);
-out = n.img - mm;
+out = apply_nifti_scaling(n) - mm;
 
 % reshape output
 out_rows = [-reshape(out(:,:,:,1),1,[]); -reshape(out(:,:,:,2),1,[]); reshape(out(:,:,:,3),1,[])];
@@ -83,23 +83,27 @@
 % copy template h5 file
 copyfile(fullfile(ea_getearoot, 'ext_libs', 'EasyReg', 'itk_h5_template.h5'), warp_file_out);
 
-if ~strcmp(ea_getspace, 'MNI152NLin2009bAsym')
-    % calculate TransformFixedParameters
-    spacedef = ea_getspacedef;
-    primarytemplate = [ea_space, spacedef.templates{1}, '.nii'];
-    hdr = ea_fslhd(primarytemplate);
-    TransformFixedParameters = zeros(18,1);
-    TransformFixedParameters(1:3) = [hdr.dim1; hdr.dim2; hdr.dim3];
-    TransformFixedParameters(4:6) = [-hdr.sto_xyz1(4); -hdr.sto_xyz2(4); hdr.sto_xyz3(4)]; % RAS to LPS applied
-    TransformFixedParameters(7:9) = [hdr.pixdim1; hdr.pixdim2; hdr.pixdim3];
-    TransformFixedParameters(10:18) = [-hdr.sto_xyz1(1:3)'/hdr.pixdim1; -hdr.sto_xyz2(1:3)'/hdr.pixdim2; hdr.sto_xyz3(1:3)'/hdr.pixdim3]; % RAS to LPS applied
-
-    % update TransformFixedParameters in h5
-    h5write(warp_file_out, "/TransformGroup/0/TransformFixedParameters", TransformFixedParameters);
-end
+% update TransformFixedParameters in h5
+h5write(warp_file_out, "/TransformGroup/0/TransformFixedParameters", ea_field_ref2itk(warp_file_in));
 
 % save TransformParameters in h5 
 h5create(warp_file_out, "/TransformGroup/0/TransformParameters", numel(out_column));
 h5write(warp_file_out, "/TransformGroup/0/TransformParameters", out_column);
 
 end
+
+
+function img = apply_nifti_scaling(nii)
+
+img = double(nii.img);
+slope = double(nii.hdr.dime.scl_slope);
+intercept = double(nii.hdr.dime.scl_inter);
+
+if isfinite(slope) && slope ~= 0
+    if ~isfinite(intercept)
+        intercept = 0;
+    end
+    img = img .* slope + intercept;
+end
+
+end
diff --git a/ext_libs/SynthMorph/ea_synthmorph.m b/ext_libs/SynthMorph/ea_synthmorph.m
index 67ca318b3..cb7c89a72 100644
--- a/ext_libs/SynthMorph/ea_synthmorph.m
+++ b/ext_libs/SynthMorph/ea_synthmorph.m
@@ -64,7 +64,7 @@
 
 function [] = freesurfer_nii_to_itk_h5(warp_file_in, warp_file_out)
 
-% substract mm coordinates for each voxel
+% Subtract millimeter coordinates for each voxel
 n = load_nii(warp_file_in);
 out = n.img;
 
@@ -75,20 +75,8 @@
 % copy template h5 file
 copyfile(fullfile(ea_getearoot, 'ext_libs', 'EasyReg', 'itk_h5_template.h5'), warp_file_out);
 
-if ~strcmp(ea_getspace, 'MNI152NLin2009bAsym')
-    % calculate TransformFixedParameters
-    spacedef = ea_getspacedef;
-    primarytemplate = [ea_space, spacedef.templates{1}, '.nii'];
-    hdr = ea_fslhd(primarytemplate);
-    TransformFixedParameters = zeros(18,1);
-    TransformFixedParameters(1:3) = [hdr.dim1; hdr.dim2; hdr.dim3];
-    TransformFixedParameters(4:6) = [-hdr.sto_xyz1(4); -hdr.sto_xyz2(4); hdr.sto_xyz3(4)]; % RAS to LPS applied
-    TransformFixedParameters(7:9) = [hdr.pixdim1; hdr.pixdim2; hdr.pixdim3];
-    TransformFixedParameters(10:18) = [-hdr.sto_xyz1(1:3)'/hdr.pixdim1; -hdr.sto_xyz2(1:3)'/hdr.pixdim2; hdr.sto_xyz3(1:3)'/hdr.pixdim3]; % RAS to LPS applied
-
-    % update TransformFixedParameters in h5
-    h5write(warp_file_out, "/TransformGroup/0/TransformFixedParameters", TransformFixedParameters);
-end
+% update TransformFixedParameters in h5
+h5write(warp_file_out, "/TransformGroup/0/TransformFixedParameters", ea_field_ref2itk(warp_file_in));
 
 % save TransformParameters in h5 
 h5create(warp_file_out,"/TransformGroup/0/TransformParameters", numel(out_column));
diff --git a/helpers/ea_field_ref2itk.m b/helpers/ea_field_ref2itk.m
new file mode 100644
index 000000000..79c2456a7
--- /dev/null
+++ b/helpers/ea_field_ref2itk.m
@@ -0,0 +1,25 @@
+function TransformFixedParameters = ea_field_ref2itk(reference_image)
+%EA_FIELD_REF2ITK Build ITK displacement-field fixed parameters from a NIfTI grid.
+
+hdr = ea_fslhd(reference_image);
+
+spacing = [hdr.pixdim1, hdr.pixdim2, hdr.pixdim3];
+if any(~isfinite(spacing)) || any(spacing <= 0)
+    error('Invalid voxel spacing in reference image: %s', reference_image);
+end
+
+stoX = hdr.sto_xyz1(1:3);
+stoY = hdr.sto_xyz2(1:3);
+stoZ = hdr.sto_xyz3(1:3);
+voxToRAS = [stoX(:)'; stoY(:)'; stoZ(:)'];
+
+rasToLPS = diag([-1, -1, 1]);
+direction = rasToLPS * voxToRAS * diag(1 ./ spacing);
+
+TransformFixedParameters = zeros(18, 1);
+TransformFixedParameters(1:3) = [hdr.dim1; hdr.dim2; hdr.dim3];
+TransformFixedParameters(4:6) = [-hdr.sto_xyz1(4); -hdr.sto_xyz2(4); hdr.sto_xyz3(4)];
+TransformFixedParameters(7:9) = spacing(:);
+TransformFixedParameters(10:18) = reshape(direction', [], 1);
+
+end