# BRIDGE Lab Documentation

## BRIDGE Lab Documentation

- [BRIDGE Lab Documentation](https://bridge-lab.gitbook.io/docs/bridge-lab-documentation.md)
- [General](https://bridge-lab.gitbook.io/docs/general.md)
- [About Us](https://bridge-lab.gitbook.io/docs/general/about-us.md)
- [Misc](https://bridge-lab.gitbook.io/docs/general/misc.md)
- [How to do misc things](https://bridge-lab.gitbook.io/docs/general/misc/how-to-do-misc-things.md)
- [Sharing Scans With Participants](https://bridge-lab.gitbook.io/docs/general/misc/sharing-scans-with-participants.md)
- [Non-Standard Printing](https://bridge-lab.gitbook.io/docs/general/misc/non-standard-printing.md)
- [Admin](https://bridge-lab.gitbook.io/docs/admin.md)
- [Onboarding](https://bridge-lab.gitbook.io/docs/admin/onboarding.md)
- [First Steps](https://bridge-lab.gitbook.io/docs/admin/onboarding/first-steps.md)
- [Research Specialist Training](https://bridge-lab.gitbook.io/docs/admin/onboarding/research-specialist-training.md)
- [Project Coordinator Training](https://bridge-lab.gitbook.io/docs/admin/onboarding/project-coordinator-training.md)
- [Offboarding](https://bridge-lab.gitbook.io/docs/admin/offboarding.md)
- [Archiving Teams Channel](https://bridge-lab.gitbook.io/docs/admin/offboarding/archiving-teams-channel.md)
- [REDCap](https://bridge-lab.gitbook.io/docs/admin/redcap.md)
- [REDCap 101](https://bridge-lab.gitbook.io/docs/admin/redcap/redcap-101.md)
- [Archiving REDCap Projects](https://bridge-lab.gitbook.io/docs/admin/redcap/archiving-redcap-projects.md)
- [Meetings](https://bridge-lab.gitbook.io/docs/admin/meetings.md)
- [Setting Up Meetings in the Conference Room](https://bridge-lab.gitbook.io/docs/admin/meetings/setting-up-meetings-in-the-conference-room.md)
- [Meeting Notes](https://bridge-lab.gitbook.io/docs/admin/meetings/meeting-notes.md)
- [Tech](https://bridge-lab.gitbook.io/docs/tech.md)
- [Effective Troubleshooting](https://bridge-lab.gitbook.io/docs/tech/effective-troubleshooting.md)
- [Remote Work Resources](https://bridge-lab.gitbook.io/docs/tech/remote-work-resources.md)
- [Servers](https://bridge-lab.gitbook.io/docs/tech/servers.md)
- [Server Permissions](https://bridge-lab.gitbook.io/docs/tech/servers/server-permissions.md)
- [Connect to an External Server](https://bridge-lab.gitbook.io/docs/tech/servers/connect-to-an-external-server.md)
- [Teams](https://bridge-lab.gitbook.io/docs/tech/teams.md)
- [Docker](https://bridge-lab.gitbook.io/docs/tech/docker.md)
- [Lynx Machines](https://bridge-lab.gitbook.io/docs/tech/lynx-machines.md)
- [Imaging](https://bridge-lab.gitbook.io/docs/imaging.md)
- [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)
- [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)
- [mSUVr](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/pet/msuvr.md)
- [Centiloids](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/pet/centiloids.md)
- [Preprocessing](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/preprocessing.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)
- [Freesurfer](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/freesurfer.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)
- [LST](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/lst.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
- [Image Analysis Log](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log.md)
- [IAM](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log/iam.md)
- [PUSH1](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log/push1.md)
- [PUSH2](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log/push2.md)
- [RISE](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log/rise.md)
- [NeuroHUB](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log/neurohub.md)
- [PUMA/CATS](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log/puma-cats.md)
- [MIND](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/image-analysis-log/mind.md)
- [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 Examples](https://bridge-lab.gitbook.io/docs/imaging/imaging-reference-guide/imaging-data-examples.md)
- [PET](https://bridge-lab.gitbook.io/docs/imaging/imaging-reference-guide/imaging-data-examples/pet.md)
- [Data Viz and Stats](https://bridge-lab.gitbook.io/docs/data-viz-and-stats.md)
- [IAM Data Pantry](https://bridge-lab.gitbook.io/docs/data-viz-and-stats/iam-data-pantry.md)
- [IAM Demographic Data](https://bridge-lab.gitbook.io/docs/data-viz-and-stats/iam-demographic-data.md)
- [Harmonization/Normalization](https://bridge-lab.gitbook.io/docs/data-viz-and-stats/harmonization-normalization.md)
- [PET Centiloids](https://bridge-lab.gitbook.io/docs/data-viz-and-stats/harmonization-normalization/pet-centiloids.md)
- [Archive](https://bridge-lab.gitbook.io/docs/archive.md)
- [MRI Data Organization \[No Longer Used\]](https://bridge-lab.gitbook.io/docs/archive/mri-data-organization-no-longer-used.md)


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