# Behavior and Neurodata Core User Manual

## Behavior and Neurodata Core User Manual

- [About](https://docs.ccv.brown.edu/bnc-user-manual/readme.md): About the Behavior and Neurodata Core
- [Infrastructure Overview](https://docs.ccv.brown.edu/bnc-user-manual/infrastructure-overview.md): Overview of BNC's Infrastructure
- [Getting Started](https://docs.ccv.brown.edu/bnc-user-manual/xnat/getting-started.md): Getting Started with XNAT
- [Accessing XNAT](https://docs.ccv.brown.edu/bnc-user-manual/xnat/accessing-xnat.md)
- [BIDS Ready Protocols](https://docs.ccv.brown.edu/bnc-user-manual/xnat/bids-compliant-protocols.md): How to name your protocols so they are easily converted to BIDS format
- [New XNAT projects](https://docs.ccv.brown.edu/bnc-user-manual/xnat/project-creation-in-xnat.md)
- [Uploading Data](https://docs.ccv.brown.edu/bnc-user-manual/xnat/uploading-data.md)
- [Uploading raw spectroscopy data](https://docs.ccv.brown.edu/bnc-user-manual/xnat/uploading-data/uploading-raw-spectroscopy-data.md): How to use our custom webapp to upload your MRS data to XNAT
- [Downloading Data](https://docs.ccv.brown.edu/bnc-user-manual/xnat/downloading-data.md): Details of the different options available to download your data from XNAT
- [Project Level De-Identification on XNAT](https://docs.ccv.brown.edu/bnc-user-manual/xnat/project-level-de-identification-on-xnat.md): XNAT allows users to attach de-identification scripts to projects using the software library DicomEdit. The script is applied to data as it is stored on XNAT, and is used to change/remove DICOM tags.
- [Introduction](https://docs.ccv.brown.edu/bnc-user-manual/demo-dataset/introduction.md)
- [How to access it](https://docs.ccv.brown.edu/bnc-user-manual/demo-dataset/how-to-access-it.md)
- [Protocol Information](https://docs.ccv.brown.edu/bnc-user-manual/demo-dataset/protocol-information.md): Explanation of BNC's Demo Dataset Protocol
- [Getting Started](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/getting-started.md)
- [XNAT2BIDS Software](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/xnat2bids-software.md)
- [Exporting to BIDS using Oscar](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar.md)
- [Oscar Utility Script](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script.md): Running XNAT2BIDS with run\_xnat2bids.py
- [Running xnat2bids using default configuration](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script/running-xnat2bids-using-default-configuration.md)
- [Running xnat2bids with a custom configuration](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script/running-xnat2bids-with-a-custom-configuration.md)
- [Syncing your XNAT project & Oscar data directory](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script/syncing-your-xnat-project-and-oscar-data-directory.md)
- [Extra tools & features](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script/extra-tools-and-features.md): We are continuing to develop run\_xnat2bids.py and xnat-tools, so please get in touch with any new feature suggestions!
- [Step-wise via Interact Session](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/using-oscar.md)
- [BIDS Validation](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/bids-validation.md)
- [Oscar](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/bids-validation/oscar.md): Running the BIDS validator on Oscar
- [Oscar - legacy validator](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/bids-validation/oscar-legacy-validator.md): Running the legacy BIDS validator on Oscar
- [Docker](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/bids-validation/docker.md)
- [Converting non-MR data](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/converting-non-mr-data.md): We are continuing to expand the types of data that can be transferred to XNAT, and exported and converted with our XNAT2BIDS software.
- [Physiological data](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/converting-non-mr-data/physiological-data.md)
- [EEG data](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/converting-non-mr-data/eeg-data.md)
- [Oscar SBATCH Scripts](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-legacy/oscar-sbatch-scripts.md)
- [Introduction to BIDS](https://docs.ccv.brown.edu/bnc-user-manual/bids/introduction-to-bids.md)
- [mriqc](https://docs.ccv.brown.edu/bnc-user-manual/bids/mriqc.md): a BIDS app that automates comprehensive quality assessment of structural and functional MRI data
- [fmriprep](https://docs.ccv.brown.edu/bnc-user-manual/bids/fmriprep.md): a BIDS app that runs a standardized and reproducible preprocessing pipeline on structural and functional MRI data
- [BIDS to NIMH Data Archive (NDA)](https://docs.ccv.brown.edu/bnc-user-manual/bids/bids-to-nimh-data-archive-nda.md)
- [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)
- [voxalign: automated MR spectroscopy voxel placement](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement.md)
- [Installation](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/installation.md): Voxalign runs on a separate computer, not the scanner console
- [Multi-session alignment](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/multi-session-alignment.md): For exact replication of voxel placement(s) within a single participant across multiple scan sessions
- [Center on MNI coordinate](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/center-on-mni-coordinate.md)
- [Quantify voxel overlap](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/quantify-voxel-overlap.md)
- [dicomsort: a tool to organize DICOM files](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/dicomsort-a-tool-to-organize-dicom-files.md): Reading DICOM files exported from the scanner or XNAT is not always intuitive. This script aims to ease confusion by organizing the files in a way that is clear and consistent.
- [ironmap](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/ironmap.md)
- [convert enhanced multi-frame DICOMs to legacy single-frame](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/convert-enhanced-multi-frame-dicoms-to-legacy-single-frame.md)
- [DICOM anonymization](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/dicom-anonymization.md): This script copies a directory of DICOMs, making modifications to the DICOM headers as specified in a configuration .csv file
- [Calculating SNR and TSNR using AFNI](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/calculating-snr-and-tsnr-using-afni.md)
- [MRI simulator room](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/mri-simulator-room.md): The MRI simulator room is a great place to train participants and acclimate them to the scanner environment.
- [Motion Trainer: Balloon Task](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/mri-simulator-room/motion-trainer-balloon-task.md)
- [Simulating scanner triggers](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/mri-simulator-room/simulating-scanner-triggers.md): Sometimes when testing stimulus code in the simulator room, it is helpful to receive regular "triggers" just as you would from the scanner every TR. We can do this with a trigger generator!
- [Stimulus display & response collection](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/stimulus-display-and-response-collection.md)
- [Eyetracking at the scanner](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/eyetracking-at-the-scanner.md)
- [Exporting data via scannershare](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/exporting-data-via-scannershare.md): External drives should no longer be plugged into the scanner console
- [EEG in the scanner](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/eeg-in-the-scanner.md): How to position the EEG equipment in the MR scanner bore for concurrent EEG-MRI
- [Exporting spectroscopy RDA files](https://docs.ccv.brown.edu/bnc-user-manual/mrf-guides/exporting-spectroscopy-rda-files.md)
- [MRF/BNC user community meetings](https://docs.ccv.brown.edu/bnc-user-manual/community/mrf-bnc-user-community-meetings.md)
- [Motion Trainer User Guide](https://docs.ccv.brown.edu/bnc-user-manual/motion-trainer/motion-trainer-user-guide.md)
- [Getting Started](https://docs.ccv.brown.edu/bnc-user-manual/motion-trainer/motion-trainer-user-guide/getting-started.md): This guide will help you quickly set up and run your first session. You'll learn how to launch the app, adjust basic settings, and try out the different movement-based games.
- [Customizing Your Settings](https://docs.ccv.brown.edu/bnc-user-manual/motion-trainer/motion-trainer-user-guide/customizing-your-settings.md)
- [Advanced Settings](https://docs.ccv.brown.edu/bnc-user-manual/motion-trainer/motion-trainer-user-guide/advanced-settings.md)
- [Adding Your Own Videos and Images](https://docs.ccv.brown.edu/bnc-user-manual/motion-trainer/motion-trainer-user-guide/adding-your-own-videos-and-images.md)
- [Motion Trainer Hardware Setup](https://docs.ccv.brown.edu/bnc-user-manual/motion-trainer/motion-trainer-user-guide/motion-trainer-hardware-setup.md): These instructions are specific to those using the Motion Trainer in the Brown University MRF's Simulator Room.