fMRIPrep poor registration between functionals and anatomical

emdupre · September 24, 2019, 6:12pm

To answer your questions:

It depends on how you called fMRIPrep. With the t2s_coreg flag, the calculated T2* map is used for coregistration. Otherwise, the appropriate “bold_ref_brain” is supplied here based on your exact call:

poldracklab/fmriprep/blob/c7c428c1277f7cee68a5de858768d8544b4ad55a/fmriprep/workflows/fieldmap/base.py#L7


# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
.. _sdc_base :


Automatic selection of the appropriate SDC method
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


If the dataset metadata indicate tha more than one field map acquisition is
``IntendedFor`` (see BIDS Specification section 8.9) the following priority will
be used:


  1. :ref:`sdc_pepolar` (or **blip-up/blip-down**)


  2. :ref:`sdc_direct_b0`

Of note, multi-echo does not currently take advantages of eg SBRef images, although there is an open niworflows PR from @tsalo to patch this. See: https://github.com/poldracklab/fmriprep/issues/1745

I think that would be a complicated bit of workflow surgery, although it’s not technically impossible. I’m not the best person to advise on exactly how to achieve that, though.

I wanted to follow up with a few questions:

Could you share your exact call of fMRIPrep ? What kinds of images are you supplying (i.e., do they have accompanying SBRefs) ?
Could you share an example reporting showing poor coregistration ? It might help to see if it’s similar to that reported by @markushs in Fmriprep handling of multi-echo data with single-band reference scans.

Thanks !

Elizabeth