SPM volume registration method

Avigayil · March 21, 2023, 6:26pm

Hi,

What is the default method used in SPM when used through brainstorm for estimating the transformation to register two MRI volumes?

Very time sensitive so if anyone has any ideas please let me know!

Thanks

Avigayil

Francois · March 22, 2023, 9:39am

'coreg.estimate', and optionally 'coreg.write'.
See code of mri_coregister.m:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/anatomy/mri_coregister.m#L110


      
          
          % === SAVE FILES IN TMP FOLDER ===
          bst_progress('text', 'Saving temporary files...');
          % Get temporary folder
          TmpDir = bst_get('BrainstormTmpDir', 0, 'spmcoreg');
          % Save source MRI in .nii format
          NiiSrcFile = bst_fullfile(TmpDir, 'spm_src.nii');
          out_mri_nii(sMriSrc, NiiSrcFile);
          % Save reference MRI in .nii format
          NiiRefFile = bst_fullfile(TmpDir, 'spm_ref.nii');
          out_mri_nii(sMriRef, NiiRefFile);
          
          % === CALL SPM COREGISTRATION ===
          bst_progress('text', 'Calling SPM batch...');
          % Code initially coming from Olivier David's ImaGIN_anat_spm.m function
          % Initial translation according to centroids
          % Reference volume
          Vref = spm_vol([NiiRefFile, ',1']);
          [Iref,XYZref] = spm_read_vols(Vref);
          Iindex = find(Iref>max(Iref(:))/6);
          Zindex = find(max(XYZref(3,:))-XYZref(3,:)<200);