Skip to content

Fix ITK displacement field metadata for EasyReg and SynthMorph #1345

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Mojackhak wants to merge 1 commit into
base: develop
Choose a base branch
from
Open

Fix ITK displacement field metadata for EasyReg and SynthMorph #1345

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 21 additions & 17 deletions ext_libs/EasyReg/ea_easyreg.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,[])];
Expand All @@ -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
18 changes: 3 additions & 15 deletions ext_libs/SynthMorph/ea_synthmorph.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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));
Expand Down
25 changes: 25 additions & 0 deletions helpers/ea_field_ref2itk.m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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