Preclinical approach
Manual steps for VBM, T2 map, DTI image sets
Convert data
Put into folders
Line up images to anterior commisure
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The automated steps
VBM
Segment and normalise using the batch I emailed
Smooth
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T2 map
Create t2 map
Segment and normalise using the batch I emailed. Maybe use first T2 image of t2 map to create normalisation parameters?
Smooth
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DTI
Create MD, FA etc maps
Segment and normalise using the batch I emailed and using the b0 image
Apply normalisation parameters to M