Transforming ROI masks to fit fMRIPrep output


I’m working with output from fMRIPrep, in the default output space (MNI152NLin2009cAsym, native resolution; 3x3x4 in this case). I have some binary ROI masks in another standard space (MNI152NLin6Asym, 2x2x2 resolution). I’m aiming to use these ROIs with my fMRIPrep output in FSL Featquery, but before I do so want to tranform the ROIs to fit the fMRIPrep output data. Is there any way to make use of fMRIPrep outputted subject-specific transform files (ending ‘_xfm’) to do this? Or, ideally, is there a way to get fMRIPrep to output different transform files that could be used to transform directly between these different standard spaces? I want to preserve the shape and location of my ROIs as much as possible, but attempts so far with ANTs and FLIRT have ended up distorting them somewhat.

Any advice would be much appreciated!


Hi @nicksouter,

You can use --output-space MNI152NLin6Asym:res-2 and get your data in that space and resolution. Additionally, if you just need the T1w-to-MNI152NLin6Asym transform files (which you can combine with transform files you already have), you might be able to get that with the --level minimal flag.