# Imaging

- [Project Lifecycle](https://bridge-lab.gitbook.io/docs/imaging/project-lifecycle.md)
- [Image Acquisition](https://bridge-lab.gitbook.io/docs/imaging/image-acquisition.md)
- [Generic MRI SOP](https://bridge-lab.gitbook.io/docs/imaging/image-acquisition/generic-mri-sop.md)
- [ViSTa](https://bridge-lab.gitbook.io/docs/imaging/image-acquisition/vista.md)
- [Data Organization](https://bridge-lab.gitbook.io/docs/imaging/data-organization.md)
- [General Documentation](https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation.md)
- [Data - First Steps](https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/data-first-steps.md): The first step in any image analysis pipeline is actually acquiring the data. After data is acquired at the scanner, it is pushed to a server called CBIHome.
- [BIDS Data Organization](https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/bids-data-organization.md)
- [About BIDS](https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/bids-data-organization/about-bids.md)
- [Raw Data](https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/bids-data-organization/raw-data.md)
- [Derivatives](https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/bids-data-organization/derivatives.md)
- [MRI Data Organization \[No Longer Used\]](https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/mri-data-organization-no-longer-used.md)
- [Study-Specific Guides](https://bridge-lab.gitbook.io/docs/imaging/data-organization/study-specific-guides.md)
- [IAM](https://bridge-lab.gitbook.io/docs/imaging/data-organization/study-specific-guides/iam.md)
- [PUSH](https://bridge-lab.gitbook.io/docs/imaging/data-organization/study-specific-guides/push.md)
- [RISE/NeuroHUB](https://bridge-lab.gitbook.io/docs/imaging/data-organization/study-specific-guides/rise-neurohub.md)
- [Image Analysis](https://bridge-lab.gitbook.io/docs/imaging/image-analysis.md)
- [General Concepts](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts.md)
- [Coordinate Systems](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/coordinate-systems.md)
- [Image QC](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/image-qc.md)
- [Raw Data QC](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/image-qc/raw-data-qc.md)
- [Diffusion QC](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/image-qc/raw-data-qc/diffusion-qc.md)
- [T1/T2 QC](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/image-qc/raw-data-qc/t1-t2-qc.md)
- [ViSTa QC](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/image-qc/raw-data-qc/vista-qc.md)
- [Spectroscopy QC](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/image-qc/raw-data-qc/spectroscopy-qc.md)
- [PyDesigner QC](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/general-concepts/image-qc/pydesigner-qc.md)
- [fMRI](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/fmri.md)
- [Misc](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/misc.md)
- [Other Pipelines](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/misc/other-pipelines.md)
- [MRS](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/mrs.md)
- [MRS Voxel Masking](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/mrs/mrs-voxel-masking.md)
- [PET](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/pet.md)
- [Preprocessing](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/preprocessing.md)
- [Freesurfer](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/preprocessing/freesurfer.md)
- [LST](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/preprocessing/lst.md)
- [PyDesigner](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/preprocessing/pydesigner.md)
- [Denoising UNI MP2RAGE Images](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/preprocessing/denoising-uni-mp2rage-images.md)
- [Registration](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/registration.md)
- [DTI-TK](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/registration/dti-tk.md)
- [TBSS](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/registration/tbss.md)
- [Segmentation](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation.md)
- [Gross White Matter Estimation](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/gross-white-matter-estimation.md)
- [NOMIS](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/nomis.md)
- [TractSeg](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/tractseg.md)
- [TractSeg + Within-Subject Registration](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/tractseg/tractseg-+-within-subject-registration.md)
- [ViSTa](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/vista.md): Written by Dr. Hunter Moss
- [Imaging Reference Guide](https://bridge-lab.gitbook.io/docs/imaging/imaging-reference-guide.md)
- [Imaging Library](https://bridge-lab.gitbook.io/docs/imaging/imaging-reference-guide/imaging-library.md)
- [Imaging Glossary](https://bridge-lab.gitbook.io/docs/imaging/imaging-reference-guide/imaging-glossary.md)
- [Imaging Data](https://bridge-lab.gitbook.io/docs/imaging/imaging-reference-guide/imaging-data.md)
- [PET](https://bridge-lab.gitbook.io/docs/imaging/imaging-reference-guide/imaging-data/pet.md)


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