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Allows for the prior execution of FSL topup, e.g. leveraging an external tool such as Synb0-DISCO, then having dwifslpreproc utilise those data internally.
When importing an existing topup output field spline coefficients image, perform a file copy rather than an mrconvert call, in order to preserve NIfTI intent codes required by applytopup.
jdtournier
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Seems fine, though I've not had a chance to test. I guess since this is going to dev, it'll get further testing before being released, so happy enough to merge. 👍
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Request has been raised a couple of times, and may well prove useful locally for processing some historical data, so figured I'd just do it.
-topup_filesoption (and indeed if they specify-eddy_options " ... --topup= ...") allows the user to specify a location wheretopuphas already been run, anddwifslpreprocwill import the two necessary files, and otherwise proceed as normal as iftopuphad been run internally, e.g. performing an initial EPI distortion correction for the sake of producing a brain mask foreddy. The path specified by the user can be thetopupoutput prefix, or one of the two files, anddwifslpreprocwill find both files automatically.Primarily to enable interfacing with Synb0-DISCO, as its principal output is the results of
topupbut its interface just about precludes its execution from withindwifslpreproc, so running that first anddwifslpreprocsecond makes more sense.Also added some option groups to the
dwifslpreprochelp page while I was at it, since it's likely to continue getting more complex over time.Closes #2144.