Hello,
I have been trying to register within-subject T1 (full brain, FOV: 192x256x160, 1mm isotropic, ACPC orientation) to T2 (smaller FOV: 512x42x512, 0.4x0.4x2mm voxels, oblique angle to optimize hippocampal resolution) scans. I don't want to move the T2 scans since we want to maintain high resolution coronal hippocampal slices for segmentation.
I've tried using FLIRT to register the T1 to the T2, which works fine, but resamples the T1 to the smaller FOV and lower resolution along the axial and saggital planes, which I don't want. So I generated the transformation matrix, and then applied it with the T1 as both the input and reference images, to preserve the FOV and resolution:
flirt -in T1.nii -ref T2.nii -dof 6 -omat T1toT2.mat
flirt -in T1.nii -ref T1.nii -out rT1.nii -init T1toT2.mat -applyxfm
But when I do this, the output image is not aligned properly to the T2.
(I also tried registering the T2 to the T1, inverting the transformation and applying it to the T1 and I get the same result).
Thanks for any help you can provide,
Jessica
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