Missing EstimatedTimeReadout on Phillips machine for DTI data : FSL topup still possible?

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Hello!

I am currently preprocessing some opposite phase encoding DTI subjects. (Bids format, AP-PA) I am using the ENIGMA DTI preprocessing protocole. I am trying to do an EPI susceptibility correction. My data is from different sources.

I am doing FSL topup if they have opposite phase encoding data and the EstimatedTimeReadout (for the acquisition parameters text).

I am using Synb0-Disco if they don’t have opposite phase encoding data but have the EstimatedTimeReadout (for the acquisition parameters text).

I am using ANTS T1w registration described here: ENIGMA-DTI-Preprocessing-Guidelines/last_resort_epi_corr at master · ENIGMA-git/ENIGMA-DTI-Preprocessing-Guidelines · GitHub if my subject doesn’t have opposite phase encoding data and the EstimatedTimeReadout (for the acquisition parameters text).

I have some subjects with opposite phase encoding but no EstimatedTimeReadout so I can’t do FSL topup. Is there a way to calculate the EstimatedTimeReadout or another method I can use?

I also wanted to know if it’s still possible to compare the data between these three types of EPI susceptibility correction if I added them as a covariable?

Thank you!

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Hi @emoann00, I’m not an expert in using topup/eddy, but the topup FAQ implies that you may still be able to use topup+eddy simply by setting the readout time to a “reasonable” value: Frequently asked questions - FSL - FMRIB Software Library

Using an incorrect value for the readout time will only cause problems if you need to use the estimated field with any software that expects it to be in Hz.

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Thank you so much! I will definitely do that for my fsl topups then!

Do you happen to know if I can do the same thing with Synb0-Disco? I am asking because I am currently using the ENIGMA ANTs registration if I don’t have the EstimatedTimeReadout for my subjects without opposite phase encoding data but it would be an interesting alternative to set a reasonable time instead of using a whole other EPI susceptibility correction method.

Thanks!

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@emoann00 I’m not sure about Synb0-DISCO, but you could always try?

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Definitely worth a try! Thanks again.

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