Hope your 2019 is going well so far; keeping with my pattern of posts I’ve got another weird one for you. Please stick with my backstory for a sec.
I’m trying to get my cog neuro department to transfer from using other preprocessing softwares to using FMRIPREP. As part of my campaign our journal club is going a practical where different groups use different softwares (e.g. FSL, AFNI, FMRIPREP) to process the same data set under different conditions because I basically said FMRIPREP would trounce them all. The conditions are:
A) Adding and removing Slice timing
B) Using different registration parameters (e.g. different T1->MNI dofs and adding or removing nonlinear warping).
My question: I know there is already a flag for slice timing and different flags for the EPI->T1 dofs and bbregistration but is there anyway in FMRIPREP to change other registration parameters for the T1->MNI warp? I’ve been pretty deep into the FMRIPREP pipeline on GitHub and this does not seem to be the case. From my explorations I think a pretty close version to antsRegistrationSynQuick default is used and ideally for the purposes of this “assignment” I’d like to mess around with, for example, removing the ‘syn’ step entirely.
My follow-up question: Given that I don’t think this is an option in FMRIPREP do you happen to know which file in the working directory essentially gets outputted having gone through every step up until this point? So since we’ll be running the default pipeline for this assignment I suppose is there a file that has gone through slice timing and motion correction but NOT registration so I can just take that file and run antsRegistration separately with different parameters to show people the differences?
I want to make clear that I am aware - and will be teaching the group - that when ACTUALLY using FMRIPREP there will probably not be a need to do this, making the entire exercise a moot point but figured I should at least try some semblance at meeting the criteria of the assignment to get my point across.