search

PennLINC / qsiprep

Preprocessing of diffusion MRI
http://qsiprep.readthedocs.io
BSD 3-Clause "New" or "Revised" License
138 stars 55 forks source link

Custom Reconstruction With Other Preprocessing Derivatives #173

Closed tjhendrickson closed 8 months ago

tjhendrickson commented 4 years ago

Hello,

Perhaps I missed this within the readthedocs page or within the issues raised on GitHub, but I am curious whether qsiprep can accept derivatives from other processing pipelines as input into the reconstruction pipeline. The reason I ask is that a data set that I would like to analyze already has extensively processed diffusion data through the HCP pipeline. If possible I would like to link these outputs directly into the reconstruction pipeline in order to eventually get estimates of structural connectivity based on one of the canned atlases provided.

Best,

-Tim

mattcieslak commented 4 years ago

Hi Tim, We haven't tried ingressing HCP pipeline output yet, but it sounds like this might be a common use case. The major issue with the connectivity pipelines is that we're expecting ANTs transforms to template space to get atlas regions aligned with the DWI data. Would calculating new registrations to MNI be a dealbreaker for you?

tjhendrickson commented 4 years ago

I don't think so!

bwinsto2 commented 3 years ago

Another option is running hcp2bids on hcp unprocessed data and then running qsiprep and reconstruction on that 🤷‍♂️

tjhendrickson commented 3 years ago

Have there been any updates on this? Is there anything I can do to help?

mattcieslak commented 8 months ago

Works for UKB now!