Add high-level brain MRI transforms for preprocessing
See original GitHub issue🚀 Feature
Add some high-level brain MRI transforms for preprocessing.
Motivation
Arguably, there are three preprocessing steps performed on most multimodal neuroimaging studies:
- Coregistration of the different modalities
- Brain segmentation/skull-stripping
- Registration to a reference space, typically MNI
I typically use NiftyReg for registration and ROBEX for brain extraction. As discussed with @ReubenDo, other modern, robust and more Python-friendly tools that could be used for this are SimpleElastix or ANTsPy for registration and HD-BET for brain extraction, similar to what’s done in MRIPreprocessor.
A related transform that might be useful is a defacing transform. The simplest way to do this is using a mask defined in the MNI space, therefore this is very related to the MNI registration.
Pitch
Add new preprocessing transforms, not meant to be used during training. Some ideas: BrainExtraction
, ToMNI
, Coregister
. The requirements would be optional, rising an error with an informative message asking the user to install them using pip
.
@romainVala, do you think this would be useful?
Issue Analytics
- State:
- Created 3 years ago
- Reactions:1
- Comments:20 (19 by maintainers)
Top GitHub Comments
and @GReguig or I will also do a PR for a new motion transform, (with coregistration, among other adds) but still a few things to finish first …
Looking forward to those papers! TorchIO has received a couple of citations from ARAMIS, but not from the CENIR 😃