Hello,
I am using mcflirt with some mouse data. The voxel size is 150 microns isotropic, and a mouse head is about 20mm long in total. Unsurprisingly, mcflirt does not work well because of the default 8mm initial search distance.
If I edit the nifti headers to multiply the dimensions up by 10 (to 1.5mm isotropic), then mcflirt works well. Is there a way I can specify the mcflirt search distances so I can avoid this tedious step?
Thanks,
Toby
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