Dwi pre-processing, no reverse phase-encoding scans

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Hi MrTrix experts,

I have a query relating to the initial pre-processing steps of DWI. Currently I have a dataset containing no reverse phase-encoding scans and solely have nii.gz images in the AP direction. Is it possible for me to continue the processing of these images (e.g. dwidenoise/dwifslpreproc etc…) and still have a reliable and valid analysis?

BW, YJP

1 Like
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Hello,

If you have a high resolution anatomical scan, it is possible to use this for the distortion correction using the SynB0-DISCO method. Presently dwifslpreproc does not have the option to directly use those outputs (TOPUP field coefficients), so you will have to call eddy yourself with the appropriate inputs. I believe this will change in an upcoming release.

From my own simulations, this method seems to work better than using a gradient echo fieldmap. I will leave the reliability and validity question to the methods people :slight_smile:

Let me know if you need any more details on how to script this.

Cheers,
Nick

1 Like
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Hi Nick,

Thank you so much for your input! It’s been very useful. If I may take you up on the matter, could you please provide some more details on how to script this in bash?

Kind Regards,
Yuscah

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DM-ed you!

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Dear Mr Trxix experts,
I met the same question, my data only has a b0 value in the AP direction. Could you please provide some more details on how to script the Synb0-DISCO in bash?

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Hello,

I also have similar issue.

I only have single PE direction diffusion MRI data and also I don’t have T1 weighted images. How can I remove distortion? Thank you very much.

I am waiting for your kind response.

Warm Regards,
Suren

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Hi Nick,
Thank you for providing this useful repository. I have tried it and succeded getting Outputs. However, after runnig, I have some trouble runnning eddy command. Is there some trouble shooting way?

TKimura