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mkdocs.yml
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site_name: CDNI's Brain
theme: readthedocs
plugins:
- search
docs_dir: docs
nav:
- Overview:
- Table of Contents: index.md
- About: about.md
- MSI:
- Getting Started: msi-login.md
- Tier 1 (High-Performance Computing) Resources: hpc.md
- Loading Software with Modules: modules.md
- Data Storage/Tracking: storage.md
- Submitting Jobs with SLURM: partitions.md
- Tier 2 (S3): s3.md
- Tips & Tricks: roadblocks.md
- Using Slurm:
- Slurm Commands: slurm.md
- Slurm Jobs: slurm-params.md
- Cronjobs: scron.md
- Resource Optimization: optimizing.md
- Software Environments:
- VS Code: vscode.md
- Miniconda Environments: miniconda.md
- Software Versioning: versioning.md
- Containers: containers.md
- Virtual Machine: vm.md
- Coding Standards:
- Best Practices: coding-practices.md
- GitHub:
- Beginner's Guide: github-quick-guide.md
- Common Git Commands: git-commands.md
- Tips and Tricks: github-tips.md
- History Scrub: github-scrub.md
- BIDS:
- DICOM to BIDS conversion: dcm2bids.md
- BIDS Validation: bids.md
- BIDS Directory Structure: bids-directory-structure.md
- Data prep:
- NORDIC Denoising: nordic.md
- Infant Preprocessing: infant-preproc.md
- Defacing: defacing.md
- 10.5T NHP ABCD BIDS Pipeline Synth: preprocessing.md
- Fast Track QC Comparison (ABCD): fasttrack.md
- Respiration Rate Settings: resp-rate.md
- Data Processing:
- Pipelines: pipelines.md
- S3 Pipeline Wrappers: wrappers.md
- Infant Pipeline Documentation: infant-doc.md
- DCAN-infant Templates/Atlases: dcan-infant-templates.md
- Running nnUNet Predict: nnunet.md
- Best Practices: processing-sop.md
- Post-processing:
- file-mapper: filemapper.md
- Precision Mapping Wrapper: precision.md
- Processing Status: status.md
- Error Query: error_query.md
- Infant Quality Assessment: infant-qa.md
- Analyzing Motion Regressors: motion-regressor.md
- Troubleshooting:
- Troubleshooting and Image Viewing: troubleshooting.md
- Testing BIBSnet: bibsnet-testing.md
- Requests and Questions: requests.md
- Quality Control:
- BrainSwipes: brainswipes.md
- Data Uploads and Transfers:
- Data Transfers: uploads.md
- Transfer ABCC Data to the NGDR: ngdr-transfer.md
- NDA Uploads:
- Managing Data on the NDA: nda.md
- Segmentation Model:
- Model Training: training-nnunet.md
- Lab Resources:
- Basecamp: basecamp.md
- Recorded Presentations: presentations.md
- UMN Recommended Courses: courses.md
- UMN Computer Installs: installs.md
- ZENODO: zenodo.md
- Plotting Tools:
- Figure Maker: figure-maker.md
- Connectivity Matrices: matrices.md
- Skinny Plot: skinny-plot.md
- Analysis Tools:
- Cifti Conn Matrix: cifti-matrix.md
- Seed Map Parcellation Wrapper: seed-map.md
- Template Matching: template-matching.md
- F Conn Regression: f-conn.md
- BWAS: bwas.md
- Calculating Rest Minutes Pre- and Post-Motion Correction: rest_minutes_motion_correction_calculation.md
- PHI:
- A Quick Guide on Protected Health Information (PHI): phi-quick-guide.md
- MR Image:
- MR-Image-Translation: mr-image-translation.md
- Contributions:
- Contributors and Papers: contributions.md
- THANK YOU FOR USING THE BRAIN:
- _____: blank.md