Run fieldmapless distortion correction on its own

[KirkGraff]

Hi all,
I'm trying to compare different ways to preprocess my data, and I'm wondering if it is possible to run only fieldmapless susceptibility distortion correction without all the other steps of fMRIprep? I'm hoping I can input an already skull stripped T1 file and a bold file and obtain a distortion corrected bold file (with a transformation matrix).

Also, would it be better to use an already motion corrected bold file, or the raw bold file?

Thanks!

-Kirk

[effigies]

Hi @KirkGraff not easily. The steps involve transforming an atlas of average distortions that's in MNI space into the individual space, which requires spatial normalization of the T1w image to already have been run.

You can check out the documentation of that sub-workflow, and see if it's reasonable for you to provide all of the inputs. If so, it wouldn't be too hard to write a small script that would take those inputs and produce those outputs, but your job wouldn't be done, there. That corrects one volume, and provides a transformation that can be applied to any volume in that space. To run it on an entire series of images, you would need to register each volume to the same reference (possibly a single-band reference, or some image derived from the series), and ideally apply the SDC in the same step.

[mattcieslak]

This would be a great niflow

[oesteban]

We have implemented the first half of the problem - estimation. I'll leave this issue open for the second half, although the priority would be very low at this point.