FreeSurfer execution when both T2w and FLAIR present

[Lestropie]

What would you like to see added in fMRIPrep?

When both T2w and FLAIR acquisitions are present (both high resolution isotropic) in the input session, it is necessary to select which to provide to FreeSurfer recon-all, given that it only supports one additional contrast. In conversation with @effigies it seems that in this instance the T2w image is given precedence (best I could find is here, but developers will know the relevant location in up-to-date code).

However I seem to recall that the recommendation is that where another modality can be used to augment FreeSurfer, FLAIR images are preferable to T2w (as long as they are of sufficient resolution), as they provide better pial surface contrast and that's where the T1w struggles. Unfortunately I'm struggling to find a good online reference stating such; maybe others might recall where such a statement has been made publicly?

Nevertheless wanted to list so that it doesn't get forgotten.

Do you have any interest in helping implement the feature?

Yes, but I would need guidance

Additional information / screenshots

No response

[mgxd]

This is a good point, and something to consider if/when there is any references to refer to.

For the time being - if you want to force the usage of FLAIR over T2w, you could use --ignore t2w. Though just as a note, this will ignore T2w usage for the entire workflow.

[effigies]

In any event, taking the higher resolution (where resolution = max(img.header.get_zooms()[:3])) among FLAIR and T2w probably makes the most sense.

[Lestropie]

Our T2w and FLAIR are precisely the same resolution 🤡

[effigies]

These seem relevant:

• https://www.mail-archive.com/[email protected]/msg48371.html

  In my experience, if the only goal is to improve the pial surface
  reconstruction, it is better to use a T2-SPACE-FLAIR than a T2-SPACE. Whenever
  possible, we acquire a bandwidth matched T2-SPACE-FLAIR at approximately the
  same resolution as our T1 and use this with our Freesurfer reconstructions.

• https://www.mail-archive.com/[email protected]/msg37279.html

  is there any difference from freesurfer's perspective of using T2-space or T2-space-flair?

  I've been working on that this week, and I think the answer is "yes, but
  not a lot". The FLAIR has worked better in our past tests, but I found
  some problems with the T2 code and it is working much better now, so I
  think the jury is out. We're happy to give you an alpha version if you want
  to test it and decide for yourself :)