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NUNDA Pipelines

Listed below are the automated processing pipelines currently available on NUNDA. For more about pipelies including directions for running them on your data, please download the Northwestern University Neuroimaging Data Archive "Great Leap Forward" presentation.

Structural Pipelines

• FSLDDMM: Freesurfer-Initiated Large-Deformation Diffeomorphic Metric Mapping for Subcortical Segmentation
• StdStructuralBuild: Pipeline for DICOM to analyze conversion, T1 processing and averaging, and T2 geometric distortion correction
• Freesurfer: Pipeline for running FreeSurfer
• TemplateInjection: Re-indexes surfaces so that all have common indexing, performs denoising
• ReillyPreProcessing: Pipeline for DICOM to nifti conversion and Brain Extraction of T1
• QA_Anatomical: Quality assurance pipeline for T1 scans

Functional Pipelines

• QA_EPI_Human/QA_EPI_Phantom: Pipeline for fBIRN QA of EPI scan types
• SPMAnalysis: Second-level analysis of BOLD data (requires RobustfMRIPreProcessing outputs)
• GenericBoldPreProcessing: Pipeline to pre-process BOLD scan types, includes QC
• RobustHelperFunctionsSession: Pipeline of robust helper functions
• RobustHelperFunctions: Pipeline to run robust helper functions and collect output into a single csv at the project level
• RobustfMRIPreProcessing: Pipeline for preprocessing fMRI data
• FSL_rsfMRI_AROMA: FSL preprocessing of rsfMRI data with ICA-AROMA for automatic artifact removal

Diffusion Pipelines

• QA_DTI: Pipeline for QA of DTI scan types
• StdDTIPreprocessing: Pipeline to preprocess DTI scan types
• Advanced Diffusion Preprocessing Pipeline: Advanced diffusion preprocessing pipeline which includes enhanced denoising, B0 distortion corrections and tensor creation.

Perfusion Pipelines

• StdASLProcessing: Pipeline to preprocess ASL scan types
• Automatic Vascular Territory Processing: analyzes MRI perfusion images using vascular territory ROIs
• ASL_RobustNormalization: Applies nonlinear warp field in output of RobustPipeline to ASL maps

Rodent Pipelines

• MouseSegmentation: Skull-strips and segments mouse MRI

Cardiac Pipelines

• Cardiac 4D Flow Analysis: This pipeline analyzes data acquired during cardiac 4D flow MRI

Request a NUNDA Pipeline

We are able to convert some workflows into NUNDA pipelines upon request. Please complete the form, and we will get in touch with you shortly.