Mp2rage in BIDS and FMRIPREP




I have three mp2rage files (2 with different inversion times, and 1 UNI). I have two questions:

  1. How do I incorporate these into the BIDS structure?
  2. Can FMRIPREP use mp2rage images for skull stripping and segmentation? If so, does it use the raw (inversion) images or the UNI image?

I looked for answers on online discussions/forums but didn’t find anything conclusive. The discussions were also > 6 months ago so maybe BIDS and FMRIPREP have been updated since then…?

Thanks so much!



Hi Anuya !

At this point, MP2RAGE has not yet been merged into the official BIDS specification-- it’s in the drafted Structural Acquisitions with Multiple Contrasts extension proposal, available here.

Because of that, FMRIPREP won’t use the images (to the best of my knowledge, though @ChrisGorgolewski, @oesteban would know best).

I believe that there was a brief meeting at OHBM to discuss the extension proposal (@KirstieJane was there, if I recall correctly), though I’m not sure what updates came out of that. Generally, if you’re using MP2RAGE in your research, it would be great to have your comments on the drafted specification !




YES! - Exactly as @emdupre said - @anuyapatil, it would be incredibly helpful if you could have a look through the BEP 001 extension and see if your data can fit into that proposal.

I wrote up a few notes about our in person meeting at OHBM here. Let me know if you have any questions :sparkles:


Thanks for the clarification. I had found it in the BIDS Extension proposal but wasn’t sure if there were any updates on that. This is also my first time with mp2rage but once I get comfortable with it, I would add comments to the draft.

Thanks for all your help!


If you name your files according to BEP001 FMRIPREP will pick up the T1w, but it will treat it like any other T1 weighted image. Unfortunately the unusual structure of noise created by MP2RAGE it will most likely fail at skullstripping. If you have experience in working with MP2RAGE images (especially robust skullstripping) we would love your help adding this feature to FMRIPREP.

This is a bit strange. Normally this sequence produces four files - T1 weighted, T1 map, and two inversion maps.


well the T1 map is not always there, this depends on the license on the siemens console

About mp2rage, the way we process it, is to compute the the brain mask with the second inversion time, and then we report the mask on the UNI volume and we run freesurfer on the masked image



The best way to deal with the noise structure in MP2RAGE images is to get rid of it - see

Sadly, the Siemens product recon does not include this. If you have the two inversion times as complex images (mag/phase or real/imaginary), then I’ve implemented the robust method here:

nipype interface coming soon…


I guess some of you are aware of this but…

I have not used it yet but I am fairly sure that the CBS tools ( include a module to get rid of the noise in the MP2RAGE and the nighres implemetation of the toolbox also include the skull stripping module (

Maybe this could help.