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Examples
Example Notebook Template
Diffusion Imaging
Basic Tracking with DIPY
Advanced Tracking with DIPY
TBSS Tutorial
MRtrix: Part 1
MRtrix: Part 2
MRtrix: Part 3
MRtrix3Tissue
Electrophysiology
EEG Analysis with MNE
Functional Imaging
AFNI Preprocessing
AFNI Preprocessing and GLM
AFNI Preprocessing & Group Analysis
Processing task-based FMRI with AFNI and afni_proc.py
FSL Preprocessing and GLM
Resting state with FSLnets
NiWrap and Connectome Workbench
ASLprep
DeepRetinotopy Toolbox
Nipype-SPM fMRI Analysis
fMRIprep
Nipype-FSL fMRI Analysis
Introduction to Preprocessing
FreeSurfer: mri_vol2surf
tedana: TE Dependent ANAlysis
Spectroscopy
MR Spectroscopy with LCModel
MR Spectroscopy with Osprey
Structural Imaging
FSL course - BET
Brain Extraction Tools
FreeSurfer: recon-all-clinical
FreeSurfer
QSMxT
SCT Toolbox
Workflows
Neurodesk Tools Demo
MRIQC
PyBIDS
RISE Slideshow
BIDS conversion
Nipype on Neurodesk
Basic Nipype
Papermill Slurm Job Submission
Pydra
Tutorials
Electrophysiology
Analysing EEG Data with MNE
Analysing M/EEG Data with FieldTrip
Functional Imaging
Connectome Workbench
Using fmriprep with neurodesk on an HPC
Using mriqc with neurodesk on HPC
PhysIO
A batch scripting example for PhysIO toolbox
Statistical Parametric Mapping (SPM)
Multimodal Imaging
Using MFCSC
Open Data
datalad
osfclient
Phase Processing
Quantitative Susceptibility Mapping
SWI
Unwrapping
Programming
Conda environments
Matlab
Reproducibility
Reproducible script execution with DataLad
Spectroscopy
Spectroscopy with lcmodel
Spectroscopy pipeline
Structural Imaging
FreeSurfer
Structural connectivity dMRI
Contribute
Contribute Example Notebooks
Contribute Tutorials
.md
.pdf
Workflows
Workflows
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Example notebooks demonstrating common preprocessing and workflow tools.
