Fmriprep t1 resolution ignoring template-resampling-grid?


We’ve used fmriprep 1.0.11 with the following flags.

–template MNI152NLin2009cAsym
–template-resampling-grid 2mm
–output-space template

We’re finding that the bold files *_bold_space-MNI152NLin2009cAsym_preproc.nii.gz have resolution 97x115x97, with 2mm isotropic voxels, but the anatomical *_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz is 193x229x193, with 1mm voxels.

Obviously, this makes overlaying any first-level analysis images on the subject’s anatomical a bit annoying, if you’re using a program like fslview that wants the two images to have the same dimensions (freeview works fine, though).

Is this behavior a bug, or working as intended?



This is as intended, and I would generally recommend using viewers that respect the file headers. FSLeyes should also work.


Alternatively you can point –template-resampling-grid to your T1w file. This will output your BOLD file in the desired resolution, but they will be massively upsampled consuming more disk space and taking more time to process in the modelling stages of your analysis. I would agree with @effigies and use viewers and tools that respect headers and can do resampling on the fly (fsleyes, mango, nilearn etc.)