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Pediatric template #24
It would be handy having a pediatric template as proposed in that comment (https://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases). This would probably deprecate (partially) #330.
@taehol, would you be interested in trying to implement this one (and becoming one of FMRIPREP's contributors)? We can walk you through the process.
That sounds interesting! In fact, I am not an extensive python user but bash, so not sure how much I can contribute for fMRI-PREP.
Anyway, to share what I am now working on, the pipeline I am now scripting (sorry I am not using FMRIPREP now) for baby resting data is using IBIS templates (http://www.bic.mni.mcgill.ca/autism/) for registration and IDEA's aal atlas (https://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases) for extracting time-series based on ANTs. Either works fine now. I have also tweaked ICA-AROMA script to use ANTs matrix and my own templates (in this case, I use IBIS-T1-1yr-2mm-brain template; the original template is on 1-mm space but I converted it to 2 mm simply because my baby epi is 2 mm and do not want to do up-sampling it), and so far so good for registration and reasonable the edge and csf fraction detection (however ICA-AROMA needs to be tested repeatedly).
Please let me know if there is something that I can be helpful to improve FMRIPREP pipeline.
I am trying to help get a few studies up and running with fmriprep using other templates (pediatric/neonate and macaque).
Sorry for the perhaps somewhat obvious question, but which wiki will be updated with the guide to adding new templates, the one associated with this github or the main fmriprep documentation page?