adni-to-bids Field Mapping output?

[Scott Gurney]

Hello

I am trying to use QuNex and their guide to importing using BIDS formatted data has the below screenshot.

My bids folder is similar with sub-1 = sub-ADNI002S1155 and ses-A = ses-M126 which I do not think will be an issue.

However, I do not believe I have ever seen a folder call "fmap" alongside anat and func, which I assume stands for field mapping.

Could you please help?

Thank you, Scott

[Nicolas Gensollen]

Hi Scott,

Thanks for your interest in Clinica.

I have never used QuNex but it seems to me that they expect datasets to follow the bids specifications, so you should be fine feeding the outputs of the clinica converters to it.

Indeed, the labels for the subjects and sessions do not have to be simple integers, so no problem using the ADNI labels.

However, note that we do not currently support the conversion of field maps for ADNI, which explains why you never saw a folder named "fmap" in the outputs.

I don't know what kind of processing you are trying to do, but maybe it doesn't require field maps ?

Note that there is an ongoing effort to support field map conversion for ADNI (see this issue: https://github.com/aramis-lab/clinica/issues/1044, and this PR: https://github.com/aramis-lab/clinica/pull/1119).

This is still a work in progress, but we might be able to have an alpha version "soonish" that you'd be able to try out.

If you're interested, I'll let you know when it is stable enough to be tried.

Hope this helps !

Best,

Nicolas

[Scott Gurney]

Hi Nicolas

Thank you for getting back to me.

I doubt it will be soonish enough for my needs, but I will bear it in mind.

Kind regards, Scott