> For the complete documentation index, see [llms.txt](https://docs.ccv.brown.edu/bnc-user-manual/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines.md).

# Analysis Pipelines

- [Task-Based fMRI Analysis Using AFNI](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/task-based-fmri-analysis-using-afni.md)
- [Single Subject Analysis: Visual/Motor Activation](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/task-based-fmri-analysis-using-afni/single-subject-analysis-visual-motor-activation.md): Preprocessing a single subject/session and applying a general linear model using AFNI
- [Group Analysis: Visual/Motor Activation](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/task-based-fmri-analysis-using-afni/group-analysis-visual-motor-activation.md)
- [First-Level Analysis Using afniproc.py](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/task-based-fmri-analysis-using-afni/group-analysis-visual-motor-activation/first-level-analysis-using-afniproc.py.md)
- [V1: Second-Level Analysis using gen\_group\_command.py](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/task-based-fmri-analysis-using-afni/group-analysis-visual-motor-activation/v1-second-level-analysis-using-gen_group_command.py.md)
- [Second-Level Analysis using gen\_group\_command.py](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/task-based-fmri-analysis-using-afni/group-analysis-visual-motor-activation/second-level-analysis-using-gen_group_command.py.md)
- [Freesurfer](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/freesurfer.md): FreeSurfer is a software package for the analysis and visualization of structural neuroimaging data.
- [Diffusion Weighted Imaging (DWI) Analysis](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis.md)
- [FSL topup and eddy](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis/fsl-topup-and-eddy.md): FSL offers command line tools for susceptibility distortion and eddy current correction. This is often the first step in preparing diffusion data for analysis.
- [Tractography: DSI Studio](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis/untitled.md): DSI studio is a tractography software tool that maps white matter tracts using diffusion weighted images. This tutorial will guide you in using DSI Studio to perform whole brain tractography analysis.
- [MRtrix3 for Diffusion Imaging Analysis](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis/mrtrix3-for-diffusion-imaging-analysis.md)
- [Step 1: Preprocessing](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis/mrtrix3-for-diffusion-imaging-analysis/step-1-preprocessing.md)
- [Step 2: Tractography](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis/mrtrix3-for-diffusion-imaging-analysis/step-2-tractography.md)
- [Step 3: Fixel-Based Analysis](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis/mrtrix3-for-diffusion-imaging-analysis/step-3-fixel-based-analysis.md)
- [Step 5: Building a Connectome](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/diffusion-weighted-imaging-dwi-analysis/mrtrix3-for-diffusion-imaging-analysis/step-5-building-a-connectome.md)
- [Brown University MRS Data Collection and Preprocessing Protocol](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/brown-university-mrs-data-collection-and-preprocessing-protocol.md)
- [PRESS Data Collection on Siemens XA30 System](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/brown-university-mrs-data-collection-and-preprocessing-protocol/press-data-collection-on-siemens-xa30-system.md)
- [Organizing Your Data and Preprocessing Using Osprey](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/brown-university-mrs-data-collection-and-preprocessing-protocol/organizing-your-data-and-preprocessing-using-osprey.md)
- [LC Model](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/lc-model.md)
- [Installation](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/lc-model/lcmodel.md): Installation of LCModel GUI
- [Example Run](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/lc-model/example-run.md): An example of running LCModel on a test data set
- [Running LCModel on your own data](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/lc-model/running-lcmodel-on-your-own-data.md)
- [Quantitative Susceptibility Mapping (QSM)](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/quantitative-susceptibility-mapping-qsm.md): Using the QSMxT toolbox to create whole-brain quantitative magnetic susceptibility maps
- [Multi-Echo fMRI Analysis Using tedana](https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/multi-echo-fmri-analysis-using-tedana.md)