preprocessing vector orientation

[Ariadna Albajara Sáenz]

Dear experts, I am following this processing pipeline described here http://www.diffusion-imaging.com/ and here https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide and one of the steps is checking if the vectors are correctly oriented with respect to the anatomy. My questions are: 1. Is this done only visually? by cheking the "lines"? I check as a reference the corpus callosum as shown here: http://www.diffusion-imaging.com/2014/03/dti-quality-control-part-2-tensor.html is that sufficient? 2. Is this done before and after eddy? 3. I was also wondering if brain extraction (which has to be done before topup and eddy according to https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide ) can also be done after topup and eddy. Thank you in advance, Ariadna

[Manuel Blesa Cábez]

Hi Ariadna,

I'll try to answer your questions:

1.- I'm afraid that's right, but assuming all your subjects are acquired with the same acquisition, you only should check it once. I know mrtrix provides a tool called dwigradcheck that can be useful for this, also DTI studio has his own gradient checker, but I always check it visually.

2.- You can do it before eddy. Eddy will modify the orientations a little bit, but if something is really wrong (an axis flipping for example) it will be clear before eddy as well.

3.- In all my pipelines I never do brain extraction per se, I use the mask for topup and eddy, and then I calculate it again after that, but I nevver mask the diffusion image.

I hope this helps.

Best regards,

Manuel

[Ariadna Albajara Sáenz]

Dear Manuel, 

Great, thank you very much for you answer, it was really helpful :)

Ariadna Albajara Sáenz

ariadna....@gmail.com

UR2NF - Neuropsychology and Functional Imaging Research Group

CRCN - Center for Research in Cognition and Neurosciences

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