Update fsl-topup from 2203.2 -> 2203.5?

[psadil]

What would you like to see added in fMRIPrep?

It sounds like the version of topup that is included in the fmriprep docker has a "buglet". From the topup changelog for 2203.4

even in the absence of movement, the most basal slice would get replicated at the very top. This had been reported as a bug, but I had not seen it because of the masking that is done. But it did mean that there would always be a missing slice at the top, which could have been a problem if the FOV was very tight in the slice direction. And it prevented me from outputting an unwarped image that wasn't truncated at the top and/or bottom. I have now fixed the bug, which means that my_fname_fieldmap_mag will have full FOV. I also added writing of a mean unwarped image as part of the --iout output, also with full FOV. This will be useful for creating a mask for eddy and/or dtifit. It means that for data with very tight FOV the estimated field will be slightly different, especially in the topmost slice. But the field generated by the new version will be, slightly, more accurate.

Another issue was resolved in 2203.5

There is a sanity check on readout times in the --datain/--acqp files. I recently coordinated that with eddy's sanity check, to ensure they have the same view of what is sane. But that meant that registering to a distortion free image no longer worked. And that is a valid thing to do, for example in the context of synb0-DISCO. I have now fixed it so that it allows one volume to have a readout time of zero, or almost zero.

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

No response