Is it possible to run only the functional workflow if there are no anatomical images or poor-quality anatomical images? I was going to build in a flag because there have been multiple requests for a pipeline that only does functional runs in my lab.
@mcsnyder Not as written. However, several of the functional subworkflows (BOLD reference estimation, slice-timing correction, head motion correction, fieldmap-based susceptibility distortion correction) do not use anatomical inputs. With a little work, these could be separated from coregistration and resampling. And portions of the confounds workflow do not require anatomical images (or BOLD series resampled in alignment with anatomical images).
Unfortunately, I don’t think we’re going to be able to devote much time to this in the near future, but we would be willing to consider a pull request that accomplishes this separation.
Hello, I wanted to know if there had been any progress on the issue discussed here. Is anyone still working on that front?
In my current sample, I have one participant who did not complete the whole scanning session. As a result, I only have the functional sequence. Preprocessing this run separately without T1 reference (mostly despike, motion correction, normalization) is relatively easy. However, I would not end up with the same confound file as in fmriprep. What would be the key steps needed to obtain similar confounds for future analysis?
I think in the latest versions (since 1.4(?)) it is possible to specify the native EPI as the desired output space. The option is:
“–output-spaces func”.