Combining fmriprep with ME-ICA from tedana

Hi @NRob,

I was asking myself the same question and then stumbled onto the post below From April 2019. It seems that we will have to use fMRIPrep and tedana separately as they are no longer working to integrate them together.

“The choice to not incorporate tedana denoising into fMRIPrep was a conscious one. Given that fMRIPrep is geared towards robustness – and our lingering concerns as to whether tedana denoising was (yet) able to produce robust results – we decided not to include it for now.”

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Thanks for this. It does appear that putting tenana into the current workflow of fMRIPrep has been put on the back burner.

I’m still a bit confused about what fMRIPrep is actually currently doing with ME data:

  1. the --t2s-coreg option says that if this option is not enabled, ‘standard EPI-T1 coregistration in performed using the middle echo.’ There was a post back in Aug. 2018 where @emdupre says that " --t2s-coreg would not combine the multiple echos. It’s another way to coregister the functional and anatomical data by first generating a T2* map and then coregistering the anatomical to that single image rather than to each of the echos separately."

There are posts in 2019 that talk about removing this option all together based on issues raised about this option, so I’m hesitant to use it.

So, if we don’t use this option, (2) the boiler plate says it “optimally combines” the ME data, and gives a reference to the Posse 1999 paper. Is this what fMRIPrep is doing with the ME data? What is outlined by Posse et al.?

Yes, I’d recommend against using --t2s-coreg at this time.

Optimal combination averages the data across echoes, with each voxel’s average weighted based on that voxel’s T2* value. The idea is to essentially predict what the data would be if you acquired each voxel its specific best echo time. In the tedana documentation, we have a walkthrough of optimal combination with figures that might be helpful.

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Thank you so much, @tsalo! I really appreciate the clarification about optimal combination, and the confirmation in not using --t2s-coreg. Thank you!

Hi Chris,

It seems that these paths have changed with new versions of fmriprep (I’m using 20.1.1) - could you point me toward where I can find the second transform in the fmriprep workdir?


Got my answer here: