Can fMRIPrep Handle Partial Brain Slabs for Functional Data?

[jsein]

Hi @ejdavid ,

The short answer is yes, it seems that fmriprep is able to deal with partial brain slabs. Your example is a good example, we also got an example at our lab where the alignment between a partial FOV functional image (30 slices of 2mm along the Sylvian fissure at 3T) and a full FOV T1w image worked well.

If the alignment between your bold image and the T1w is good, I would say that you are good to go!

Additional question: Do you use SDC to correct your functional images?

There were some other discussions about this subject in those threads:

Fmriprep output badly misaligned?

Partial FOV registration is challenging. Which fmriprep version are you using? You may have a look at this topic and issue therein: If you are already using the latest fmriprep version, could you try the option --bold2t1w-init header to see if you get some improvement?

Problems with fieldmap-based susceptibility distortion correction in combination with a high-resolution partial volume

I am surprised by this choice. Usually sbref images refer to the image generated from multiband sequences which has better contrast than the bold series acquired at steady-state. I think this sbref is used (when --ignore sbref is not passed as an argument) as a target for the bold realignment AND used also for the bold-to-T1 registration. I am not sure how mcflirt, the realignment function used internally by FMRIPREP would deal with a sbref image with different FOV that the BOLD images thems…