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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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Support for limited field of view #331

Open chrisgorgo opened 7 years ago

chrisgorgo commented 7 years ago

To improve temporal and spatial resolutions sometimes a limited field of view is used. In such case only preselected part of the brain is imaged. This can lead to challenges when coregistering to T1w volume. We can use the 7T TRT dataset to test any potential solution.

oesteban commented 7 years ago

Several people asked for this in the context of MRIQC as well :+1:

oesteban commented 6 years ago

Ref #899, #900, #901, #896, #895.

Make the appropriate amends to allow FMRIPREP to work correctly on these images:

suxpert commented 2 months ago

Are there any update on this topic? What is the best solution for limited FoV scans nowadays?

milenamusial commented 1 month ago

I'd be interested, too!

effigies commented 1 month ago

If your BOLD and T1w data are already in rough alignment (open as overlays in some viewer), then my recommendation would be --bold2anat-init header, which will skip the bulk registration and only perform the boundary-based registration refinement.

If they are not mostly aligned already, then you may want to use a tool like 3dslicer to manually align first.