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ins-amu / scripts

prepare data for TVB
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Take into account two DTI runs to do correction #33

Closed maedoc closed 9 years ago

maedoc commented 9 years ago

Jonathan called this a "topup" correction. I have no idea what he meant, but I suppose mrtrix can take into account two images.

timpx commented 9 years ago

topup is the fsl function to correct the current distortion induced by head movement and eddy currents. Eddy current are already corrected in scripts using the old fsl function eddy_correct. The new function topup is better, but require a specific acquisition scheme. Last time I asked, they did not had such scheme implemented in Marseille (actually they did not bother to answer my mail). If they have improvement on their side, I will be more than happy to implement it.

timpx commented 9 years ago

with the MRtrix3/mrtrix3/02ff4a8a40c8335b031ca commit and b832b1e0fb398af commit, this should now work. Please add export topup="reversed to your config file. The command takes a long time to run (around 12 hours)

maedoc commented 9 years ago

I had to restart as my oar job got cut. It seems to spend a lot of time on Running Register. This is normal?