Availability of the Harvard-Oxford atlas in MNI152NLin2009cAsym template

[oesteban]

@dlevitas

From the templateflow’s github page, I see this template option, GitHub - templateflow/tpl-MNI152NLin6Sym: Symmetric MNI152 6th generation template · GitHub, which correct me if I’m wrong, looks very similar to FSL’s MNI152 template.

As you will see in this conversation, that one looks very similar to FSL’s MNI152 but it is not quite the same thing.

We would like to include that template into TemplateFlow ASAP. We would be extremely happy to accept help in the task (that is the bottleneck at this point in time).

@dlevitas

1). Can fmriprep ( 1.3.0 or higher) accept a different template, such as the MNI152NLin6Sym?

We’ve been taking steps towards making this possible, but it is not yet there. Creating TemplateFlow (a way to dynamically pull from a pool of templates that can be selected under a controlled vocabulary of identifiers) we solved a big portion of the problem. However, the latest releases (1.3.0 and higher) have mostly addressed issues derived from TemplateFlow’s integration. It seems that 1.3.2 is giving positive signals as to whether TemplateFlow’s integration has reached acceptable reliability and now we can move on and make use of TemplateFlow’s features.

In sum, the answer to this question is not yet.

@dlevitas

2). If not, is there a way to align the Harvard-Oxford atlas ROIs to the fmriprep output? When I’ve taken the output to FSL, I’ve followed this strategy for avoiding FSL’s registration step, since it’s already been performed in fmriprep. Thinking over my issue, my thought has been to allow FSL’s registration to the MNI152 template, but this seems like an unnecessary interpolation step.

If you could allow some time for us to provide with a good solution to this (i.e. generating the Harvard-Oxford segmentation on fMRIPrep’s MNI flavor) I could commit to having this included within TemplateFlow in one week.

If you can’t wait that long, then it depends on the inaccuracy in registration you’d be willing to accept. If you don’t need submm accuracy, then just resampling the HO atlas with an identity interface would work. Otherwise, you’ll need a solution where you run some registration protocol between MNI152NLin2009c and FSL152NLin2006Asym (which is what I’ll run to provide the first solution to this question).

Finally, the best solution is to wait for fMRIPrep to leverage TemplateFlow and allow you to set FSL152NLin2006Asym as target template. That will probably take the longest time.