Hello SPM community,
I am using SPM12 (6906), and I am attempting to align a T1 structural scan to an EPI image, and apply that co-registration to a mask defined by the anatomy. So I have set the EPI as the reference, the T1 as the source, and the mask as an "other" image, and then I push play in the batch editor (with all other options set to the default values).
If I run this procedure, I do get a properly registered T1 and mask... but the source images have also been altered. It's as if the volume has been tilted 90 forward (i.e., the sagittal slice is now looking straight down, my axial view is now showing what looks like a coronal slice, and my coronal viewer is showing an "inverted" axial slice).
My expectation was that SPM would produce new, co-registered images and leave the source material alone. Does anyone have suggestions about what might be going wrong? I'm happy to provide as much information as needed, if anyone want to try and replicate. My job definition is below.
Thank you!
Chris
matlabbatch{1}.spm.spatial.coreg.estwrite.ref = {'D:\MRI\SoundPicture\data\PREPROCESS\02\MRH026_201\debug_coreg\MRH026_201_WIP_RUN_1_DE_SENSE_7_1_short.nii,1'};
matlabbatch{1}.spm.spatial.coreg.estwrite.source = {'D:\MRI\SoundPicture\data\PREPROCESS\02\MRH026_201\debug_coreg\oMRH026_201_T1W_IR_1150_SENSE_3_1.nii,1'};
matlabbatch{1}.spm.spatial.coreg.estwrite.other = {'D:\MRI\SoundPicture\data\PREPROCESS\02\MRH026_201\debug_coreg\mask_ICV.nii,1'};
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.cost_fun = 'nmi';
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.sep = [4 2];
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.fwhm = [7 7];
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.interp = 4;
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.mask = 0;
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.prefix = 'r';
spm_jobman('run', matlabbatch)
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