I have run the structural pipeline on our neonatal with relatively high success and would like to also use the fMRI pipeline. Unfortunately, I do not believe we have SBREF or spin-echo EPI images. I noticed a solution to having no Fieldmap and am hacking the script to either
- Use the scripts motion correction methods to register the func to anat
- Slot into the script our own motion corrected func in anat space
Or maybe it just be easier to write our own script to use the trained FIX classifier and not use the fMRI pipeline (unless below question 2) applies)?
My two main questions
- Has anyone faced this issue of not having SBREF. Did you edit the script to go straight from func to anat. Or, did you skip the registration process and input your own motion corrected func to anat images.
- I can get my hands on ‘DTI field maps’, can I insert these directly into the pipeline (in place of the spin-echo EPI images) or do I need to pre-process them in any way?
Thanking in advance for any advice offered!