[Neuroimaging] nipy for doing volume realignment & smoothing in real time

Michiel Cottaar michiel.cottaar at ndcn.ox.ac.uk
Thu May 20 05:57:46 EDT 2021


There are many registration tools wrapped in nipype you could choose from to register a 3D volume to a reference. Within FSL you could use fsl.FLIRT(in_file='latest_scan.nii', ref='reference.nii) .

Best wishes,


On 20 May 2021, at 10:36, David Soto <d.soto.b at gmail.com<mailto:d.soto.b at gmail.com>> wrote:

we are planning a real time fMRi experiment and would like to use nipy to do some preprocessing namely volume realignment of each incoming TR + some smoothing

however by looking at the documentation. E.g:
>>> from nipype.interfaces import fsl>
>> from nipype.testing import example_data
>>> mcflt = fsl.MCFLIRT(in_file=example_data('functional.nii'), cost='mutualinfo')
>>> res = mcflt.run()

it would seem that it would only work for  a collection of scans (i.e.the 4D file) of a run.

Would there be a way to use nipy tools to have a reference image and then each scan that is analysed in realtime to be realigned relative to that reference?

thanks for any feedback/suggestions!


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