✨ Read in field map's TotalReadoutTime for use in FSL TOPUP (distortion correction) - Githubissues

FCP-INDI / C-PAC

Configurable Pipeline for the Analysis of Connectomes

https://fcp-indi.github.io/

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✨ Read in field map's TotalReadoutTime for use in FSL TOPUP (distortion correction) #1768

Closed sgiavasis closed 8 months ago

sgiavasis commented 2 years ago

Related problem

Blip distortion correction via FSL TOPUP (uses the *_epi field maps) reads in DwellTime from the field map's meta-data in the JSON sidecars. It uses the dwell time to calculate the total readout time for use in the acquisition parameters file that is supplied to the topup commandline call.

However, some datasets have field maps that only have the TotalReadoutTime but no DwellTime listed in the meta-data. For these data, the total readout time should be easily read into topup directly. But right now, CPAC will complain that DwellTime is missing and cannot proceed.

Proposed feature

Build the plumbing to read in TotalReadoutTime from the JSON meta-data, and use that first for topup if supplied.

Acceptance criteria

[x] Working directory shows the TotalReadoutTime value present in the JSON meta-data for the field map being written into the acqparams.txt created in the FSL TOPUP workflow's phase_encode node.
[x] Sanity check against external pipeline which uses the same information to calculate the distortion correction unwarp.

Alternatives

No response

Additional context

No response

sgiavasis commented 8 months ago

This was resolved in v1.8.5.