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Here are a few lines of code that might be useful... P = spm_select(1,'nifti'); % Select an NIfTI file Nii = nifti(P); % Read NIfTI header Nii.mat % Show the sform matrix Nii.mat0 % Show the qform matrix Nii.hdr % Showing the contents of the header itself (note that you can not change the header directly) Nii.mat0 = Nii.mat; % Copying the sform to the qform Nii.mat = Nii.mat0; % Copying the qform to the sform %create(Nii); % Write (or re-write) the header to disk (commented out) For the Python or C++ users among you, note that the sform matrix is adjusted to account for MATLAB counting voxels from 1..N, rather than the 0..N-1 . This is why Nii.hdr.srow_x (or _y or _z) is slightly different from what it says in Nii.mat0 . Best regards, -John ________________________________ From: SPM (Statistical Parametric Mapping) <[log in to unmask]> on behalf of Aran Garcia <[log in to unmask]> Sent: 05 February 2020 09:56 To: [log in to unmask] <[log in to unmask]> Subject: Re: [SPM] SPM overwrites qform Dear Guillaume, May I ask how would you apply the change to the header of the images? Because we found a way, copying and pasting the "correct" numbers/orientation. Wondering whether a "better" way does exist? And yes, the troubes were created when using different softwares that prioritise the qform orientation before the sform, like FSL and ITKviewer Peace, aran