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Preparing T1 files
FSL does not read all nifti files properly, so we convert them. There was some issue with reading rotations/shears, so these are removed with reslicing. Additionally, testing on 0.65 x 0.65 x 0.0.65 mm voxel size files also needed a conversion to int16 from float 32 data format.
Manually Running and Testing
OLD: To set up FSL FIRST to run custom VOI:
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