Quantitative Brain Imaging
Course is an introduction to methods and tools used in quantitative brain imaging, including structural and functional brain imaging using magnetic resonance imaging. I recommend acquiring basic knowledge on MRI and linux/unix environment prior to the beginning of the course. Ideally user is operating in linux based environment with neuroimaging tools installed like Neuroubuntu or Neurodebian. In extreme cases cause can be conducted based on software running MS Windows operating system, however that does not provide independent capacity for comprehensive image analysis pipeline. Depending on the audience and learning objectives the course duration is variable and depends on the needs and targets of the participants.
Course structure
Module 1 - Magnetic resonance imaging - understand how the image is created and stored
Module 2 - Introduction to methods - basic skills
Module 3 - Online brain imaging databases
Module 4 - Structural brain imaging I - Gray and White matter segmentation
Module 5- Structural brain imaging II - Brain image registration
Module 6- Structural brain imaging III - Diffusion tensor imaging
Module 7 - Voxelwise structural analysis
Module 8 - Functional brain imaging (BOLD, DSC Perfusion and ASL)
For students attending the May 2017 course
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Module 1 - Magnetic resonance imaging - understand how the image is created and stored
How MRI works - basic principles
Principles of magnetic resonance imaging by Mark Puddephat
The Basics of MRI - by Joseph Hornak (very good intro to magnetic resonance)
Learn the principles using low field MRI
Paul Callaghan video lectures on magnetic resonance imaging at Magritek
02 - Introduction to Nuclear Magnetic Resonance
04 - Acquiring Free Inducation Decay
06 - Spin echos, CPMG, T2 relaxation
07 - Measuring T1 and T2 relaxation
08 - Magnetic Resonance imaging in 1D
09 - Introduction of k-space 1 and 2
Pulse sequences - what are they and how to use them?
Bitar 2006 What every radiologist should know abour MR pulse sequences
Advanced methods
Blood Oxygenation Level Dependent (BOLD) fMRI
MRI Physics tutorial by Karla Miller from FMRIB
Arterial Spin Labeling
Susceptibility weighted imaging
Vascular Space Occupancy (VASO)
Steady State sequences
Magnetic Resonance Spectroscopy (MRS)
Multinuclear MRI (Na, P etc.)
Ravinder Reddy on Multinuclear at 7T
Additional MR physics resources
Do your own MRI experiment
Virtual MRI scanner based on java from Institut fur Telematik in der Medizin
Jemris - Juelich mri scanner
SpinBench - mri sequence simulator
Optional - Design your own MRI sequence using the following sequence building tools:
ODIN - Object-Oriented Development Interface for NMR
SequenceTree - user friendly sequence development environment developed at UPenn
MRI Safety resources
The principal rule in brain imaging laboratory is the safety of subjects and staff working with magnetic resonance imaging scanner. Learn more on potential sources of injury at the MRI suite:
FMRIB MRI Safety web resources by Peter Jezzard
What happens when magnetic object enters the scanner bore
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Module 2 - Introduction to methods - basic skills
Software - general
Neurodebian Virtual Machine Installation
BrainSuite - BrainSuite homepage - LONI website - Tutorial
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Module 3 - Online brain imaging databases
Image data archives
Otwarte bazy obrazów mózgu - polish
Brain development - used to be IXI
File formats and their function
DICOM
NEMA website - official dicom description
ANALYZE
NIFTI
Brain image processing pipeline
Brain atlases
Public Brain Atlas - Brain Observatory
Spatially unbiased atlas of Cerebellum
Atlas - MRI imaging of brain and spine
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Module 4 - Structural brain imaging I - Gray and White matter segmentation
Brain atlas tools and resources
Brain structure search in polish
Probablistic atlas of the Cerebellum
Software - Brain segmentation
Brain segmentation testing protocol
Alvin - lateral ventricles segmentation
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Module 5- Structural brain imaging II- Brain image registration
Software tools for brain image registration
Brain surface analysis
Freesurfer tutorial
BrainSuite11
Cortical curve tracing in Brain Suite
BrainSuite surface file format
Notes on Brain Suite surface file format
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Module 6- Structural brain imaging III - Diffusion tensor imaging
Assessing white matter microstructure
Diffusion tensor imaging software tutorials
Diffusion model fitting and tractography
Diffusion tensor imaging: concepts and applications LeBihan 2001
Software - Diffusion tensor imaging
FDT - FSL diffusion toolbox
DTITK - Diffusion Tensor Imaging Toolkit
Camino
References
Linda J. Lanyon (2012). Diffusion Tensor Imaging: Structural Connectivity Insights, Limitations and Future Directions, Neuroimaging - Methods, Peter Bright (Ed.), ISBN: 978-953-51-0097-3, InTech, Available from: http://www.intechopen.com/articles/show/title/diffusion-tensor-imaging-structural-connectivity-insights-limitations-and-future-directions
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Module 7 - Voxelwise structural analysis
NPM
FEmap
TBSS
FSL-VBM
VBM
Continuous Medial Representation
Advanced topics
Multivoxel Pattern analysis (MVPA)
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Module 8 - Manual segmentation
Protocols for manual segmentation of brain structures
Hippocampus
Caudate nucleus
LONI caudate segmentation protocol
The caudate nucleus was traced in successive 1 mm slices in the coronal plane. The caudate was subdivided into three defined subregions: the body, head, and caudate/putamen complex (Fig. 1). Anatomical anterior and posterior boundaries for each sub-region of the caudate were traced as follows:
The Body:
anterior - slice at which one can differentiate the foramen of monroe
posterior- slice where the junction between the left and right thalamus is first visible
The Head:
anterior - slice at which one can last distinguish the internal capsule
posterior- slice anterior to the one in which the foramen of monroe can be distinguished
The Caudate/Putamen Complex:
anterior - slice where the caudate/putamen complex is no longer visible
posterior- the slice anterior to the one in which you can last distinguish the internal capsule
Pubmed search on "caudate manual segmentation"
Miccai 2007 caudate segmentation challenge
Manual segmentation protocol paper
Cerebellum
LONI cerebellum segmentation protocol
LONI manual segmentation protocols
Harvard anatomy lab protocols
Center for Morphometric Analysis - Harvard Medical School
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Module 9 - Functional brain imaging (BOLD, DSC Perfusion and ASL)
MRI courses and resources
Rik Hanson's SPM minicourse 2008
Cambridge Brain Imaging Unit Wiki
MRI Physics and Analysis for Cognitive Neuroscientists
Chris Rorden's excellent fMRI course (2011)
Washington University School of Medicine - Neuroscience tutorial
BOLD fMRI analysis software
FSL-FEAT
SPM
AFNI
VoxBo
fMRI for clinicians - by Karla Miller
Perfusion Imaging
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Resources & References
Books
Statistical Parametric Mapping
Journals
Opendata
One of the major obstacle in learning the structure and analysis of neuroscience data is the limited access to available open domain datasets. To address that issue number of groups around the world have released data that can be accessed and analyzed for learning purposes.
Neuroscience datasets
EEG/ERP data repository from UCSD
SPM datasets and tutorial data
DTI datasets from MRIStudio tutorial dataset
Neuroimaging Data Access group - NIDAG
Open Connectome - mouse brain images
Neuroscience Information Framework
National Database for Autism Research
The Child and Adolescent NeuroDevelopment Initiative (CANDI)
Other interesting data
HealthDataPalooza Video sessions BIG data discussion
Public data explorer - interesting way of using public datasets
Data archive of The Journal of Statistical Education
Statistical Science portal datasets
Public Data on Amazon Web Services
Natural Resources Conservation Services - Plants data
Central Statistical Office - Poland
Bioconductor and microarray analysis of public data
Brain imaging laboratories
PICSL
SBIA
MMRRCC
FMRIB
LONI
FIL
SPL
INRIA
Center for Interdisciplinary Brain Sciences Research
JHU Laboratory of Medical Image Computing (MEDIC)
RUBIC - Rutgers University Brain Imaging Center (access to Siemens scanner documentation)
Schnyer Learning and Memory Lab
Chris Rorden's Neuropsychology Lab
Brain Imaging projects
Human Connectome
1000 functional connectome
Courses and Tutorials
MRI-Tutorial by Niels van Strien
fMRI training online NITP summercourse videos
Neuroimaging Tools Resource Center
Neuroimaging software Utah SCI
UMK Course
Adobe Connect videoconference system
Prezentacja do wykładu dla PWr 2015-01-14
Obrazowanie ilościowe kwiecień 2018