[Neuroimaging] [fmriprep] Specifying different priors and templates

Chris Gorgolewski krzysztof.gorgolewski at gmail.com
Fri Jan 13 11:20:28 EST 2017

The documentation for new contributors is up now (along a new release):

On Tue, Jan 10, 2017 at 3:03 PM, Chris Gorgolewski <
krzysztof.gorgolewski at gmail.com> wrote:

> Hi Dan!
> It would be great to get your help! More comments below:
> On Tue, Jan 10, 2017 at 1:07 PM, Dan Lurie <dan.lurie at berkeley.edu> wrote:
>> Hey fmriprep team,
>> I am working on a pull request to add support for using lesion masks
>> during T1 registration, and wanted to check in with you guys before I got
>> too deep. A couple of questions:
>> 1) I’m assuming it’s best to create a separate new pipeline based on
>> ds005 instead of modifying ds005? I want to make sure i’m adding things in
>> a way that is consistent with the overall architecture you’ve envisioned.
> Yes this is the best way to go around it. In general FMRIPREP is looking
> at what data is available for a given subject and then applies the
> appropriate pipeline (this happens here
> <https://github.com/poldracklab/fmriprep/blob/master/fmriprep/workflows/base.py#L56>).
> So in your case you should see if there is a lesion mask available for a
> given subject and chose your new workflow instead of ds005. The selection
> of the workflow can be overridden on the commandline - os you need to add
> the name of the new workflow here
> <https://github.com/poldracklab/fmriprep/blob/master/fmriprep/run_workflow.py#L59>.
> BTW we are considering changing workflow names
> <https://github.com/poldracklab/fmriprep/issues/311> to make them more
> intuitive.
> The new workflow should reuse subworkflows of ds005 as much as it can. We
> want to minimize the amount of replicated code.
> 2) Lesion masks are usually in subject native space, so using cost
>> function masking in ANTs requires specifying the template as the moving
>> image and then using the inverse transforms (see here:
>> https://github.com/stnava/ANTs/issues/48). My plan was to just change
>> the pipeline workflow inputs/outputs to accommodate this change (e.g. use
>> the inverse transform when registering the EPI and TPMs). Is there anything
>> tricky about how the pipeline is organized that I should keep in mind when
>> doing this?
> I see. You just need to connect the output transforms to the right
> outputnode fields. You also minght need to calculat/generate inverse
> transforms.
>> 3) is run_workflow.py the place to add options/settings for things like
>> specifying what templates to use during skull stripping and tissue
>> segmentation? I looked through the BIDS-Apps docs to see if there was any
>> common design pattern established, but didn’t see anything.
> If you want to add an option to use different templates for
> BrainsExtraction doing it via a commandline parameter in run_workflow.py is
> the best option. Is the template we are using now (OASIS) not working for
> your data? Maybe we can figure out how to choose which template to use
> based on some data properties?
> Thanks in advance, and apologies if I’m missing anything obvious. Happy to
>> chat over Skype/Hangouts if that’s easier than email.
> Happy to have a chat if you want to. We should get some documentation for develeopers
> soon <https://github.com/poldracklab/fmriprep/issues/309>.
> BTW one thing I'm interested in is how did you organize your input data.
> The lesion masks are hand drawn yes? We should work on some standardized
> way of saving such data in BIDS that FMRIPREP can work with.
> Best,
> Chris
>> Dan
>> --
>> Dan Lurie
>> Graduate Student
>> Department of Psychology
>> University of California, Berkeley
>> http://despolab.berkeley.edu/lurie
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