Register the FLAIR or T2 to the T1w space

[wanjiag]

Coregister FLAIR and/or T2 into the T1w space, and add this option as derivatives for fmriprep.

[effigies]

Thanks for proposing this. I think it makes sense to do this unconditionally on FLAIR and T2w images.

Some options for registration:

1. FreeSurfer uses bbregister after surface reconstruction to align T2/FLAIR to the T1.
2. mri_robust_register has the following example in its documentation:

EXAMPLE 4
	Robust cross modal registration:
	 
	mri_robust_register --mov movT2.mgz --dst dstT1.mgz --satit --iscale 
	--mapmov T2_to_T1.mgz --lta T2_to_T1.lta --cost ROBENT --entradius 2 
	--entcorrection --weights T2_to_T1_weights.mgz
	 
	Registers a T2 image to T1 using robust entropy with correction mode 
	and box radius 2 (= side length of 5 for boxes).
	Look at results with:
	
	freeview dstT1.mgz T2_to_T1.mgz T2_to_T1_weights.mgz:colormap=heat

3. ANTs has antsIntermodalityIntrasubject.sh which implements something like this.

I suspect the biggest concern most of the time is going to be changes in neck position throwing off the cost function, which all three of these methods should handle reasonably well. There are also histogram-matching techniques, but those work better on skull-stripped brains, which adds complexity.

I would probably start by, outside of fMRIPrep, giving each of these a try and seeing whether any is obviously better or worse than the others.

Related: nipreps/fmriprep#474

[wanjiag]

This sounds good to me! Thanks for listing the potential methods. Since my data set only has T2 but not FLAIR, I am wondering if there is any open sources data set that I can try all three methods with? I assume the comparison is mostly by eye on this step?

Thanks again Chris!

[effigies]

I would check OpenNeuro. If you have datalad, you can search all of it pretty easily:

datalad install -r ///openfmri
find openfmri -name '*FLAIR.nii*'

(I actually just ran it to check, and it looks like ds000221 and ds000244 are good candidates. And a lot have T2w, as well, if you want to try some more datasets.)

And yes, this is basically by eye.

[wanjiag]

Thanks! I will follow up when I am done with this step.

[sameera2004]

Hi @wanjiag,

We are collecting both T1w and T2w data for all our fMRI studies. We are using HCP to pre process our data. Recently I started to use fMRIprep to pre process our structural and TASK data.

I found out we don't see T2w outputs after running fMRIprep. I only see T1w outputs like following

sub-500_desc-preproc_T1w.nii.gz
sub-500_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
sub-500_from-T1w_to-fsnative_mode-image_xfm.txt
sub-500_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
sub-500_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz

Do you thing it's possible to get T2w outputs like T1w's ?

Thank you
Best Regards
Sameera