Dimension mismatch among preprocessed BOLD image, smoothAROMA_bold, and the corresponding the standard template while mapping to MNI152NLin2009cAsym, fmriprep 1.4.0

1

Hi All,

I conducted the preprocess of my fMRI data using fmriprep 1.4.0.

I found there are dimension mismatched among the following data:

  • *_space-MNI152NLin2009cAsym_desc-preproc_bold (82, 97, 81 (voxel-size 2.4x2.4x2.4))
  • *_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold (91, 109, 91 (voxel-size 2x2x2))
  • tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz (97, 115, 97 (voxel-size 2x2x2))

I was wondering do the first two data normalized to the MNI152NLin2009cAsym (though when I overlay them together with the tpl by fsleyes they do look aligned, I want to make sure of this)?

For the _desc-preproc_bold, I guess the mismatch of the dimension might due to different voxel sizes. But I can’t understand the dimension mismatch between _desc-smoothAROMAnonaggr_bold and the template as they have exactly the same voxel size. Is anything wrong here? Should I reslice/resample these output from fmriprep to the tpl by myself to make them have the same dimension? (By the way, this mismatch doesn’t happen when I use the MNI152NLin6cAsym template.)

Sincerely,
Tianji

2

The mismatch is intended:

  • *_space-MNI152NLin2009cAsym_desc-preproc_bold (82, 97, 81 (voxel-size 2.4x2.4x2.4)) keeps the resolution of your original BOLD data (2.4mm isotropic)
  • *_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold (91, 109, 91 (voxel-size 2x2x2)) uses the FSL MNI template matrix (91x109x91) because AROMA was trained with that one. At some point (after 1.4.0, it seems), you’ll see that these outputs have changed to *_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold for consistency with AROMA (MNI152NLin6Asym corresponds to the MNI template shipped with FSL).
  • tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz (97, 115, 97 (voxel-size 2x2x2)) this is the original template file (i.e., it is not an fMRIPrep output).

For further details, and how to generate preprocessed data on other resolutions and matrix sizes please check https://fmriprep.readthedocs.io/en/latest/spaces.html.

3

OK. I understand now. Thank you very much for your explain.

Cheers,
Tianji