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[DOC] Document clipping of background for PetLinear #1394

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Nov 26, 2024
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[DOC] Document clipping of background for PetLinear #1394

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2 changes: 2 additions & 0 deletions docs/Pipelines/PET_Linear.md
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# `pet-linear` - Linear processing of PET images

This pipeline performs spatial normalization to the MNI space and intensity normalization of [PET](../glossary.md#pet) images.

Its steps include:

- clipping of the background to remove noisy values which can deteriorate further processing.
- affine registration to the [MNI152NLin2009cSym](https://bids-specification.readthedocs.io/en/stable/99-appendices/08-coordinate-systems.html#template-based-coordinate-systems) template [Fonov et al., [2011](https://doi.org/10.1016/j.neuroimage.2010.07.033), [2009](https://doi.org/10.1016/S1053-8119(09)70884-5)] in MNI space with the SyN algorithm [[Avants et al., 2008](https://doi.org/10.1016/j.media.2007.06.004)] from the [ANTs](http://stnava.github.io/ANTs/) software package [[Avants et al., 2014](https://doi.org/10.3389/fninf.2014.00044)]
- intensity normalization using the average [PET](../glossary.md#pet) uptake in reference regions resulting in a standardized uptake value ratio ([SUVR](../glossary.md#suvr)) map
- cropping of the registered images to remove the background
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