Download Documents & Tutorials
Talks & Tutorials
- Using docker for Deep Learning on NIRAL servers:
- Basic intro to docker, how to use NIRAL servers for Deep Learning, how to schedule the server etc [Youtube video of tutorial]
- Python tutorials for beginners
- Basic intro, how to use jupyter, loading, merging and saving csv files via dataframes in pandas: [Youtube video of tutorial], [PPT of tutorial]
- Diffusion MRI tutorial lessons as PPTX & Videos:
- Update 2022: infant diffusion MRI preprocessing: Video at Fit’NG vimeo
- Basics of diffusion, tensors, tensor properties, visualization: [DMRI_intro-Lession1], [Lesson 1 at YouTube – Intro]
- Tractography, analysis frameworks (regional, voxel/TBSS, fiber tract based): [DMRI_intro-Lession2], [Lesson 2 at YouTube – Tracts],
- Diffusion MRI QC with DTIPrep and FS 5.12/6.1: [DMRI_intro-Lesion3-QC], [Lesson 3 at YouTube – QC]
- How to build DTI atlases with DTIAtlasBuilder: [DMRI_intro-Lesson4-AtlasBuilder], [Lesson 4a at Youtube – Atlas Builder]
- Automatic tractography via AutoTract, Fiber Profiles via DTIAtlasFiberAnalyzer and FADTTSter: [DMRI_intro-Lesson4b-TractAnalysis] [Lesson 4b on Youtube – Fiber analysis]
- Higher-order models of diffusion, Diffusion structural connectivity: [DTI_intro-Lesson5-HigherOrderModels] [Lesson 5 on Youtube – Fiber analysis]
Laboratory manual ACE-IBIS Infant Study Image processing pipelines [ pdf link ]
- Image processing methods and pipelines
- Guidelines for segmentation of anatomical structures
- Geometric phantom calibration of structural MRI
Rhesus Monkey Brain Atlas: Subcortical Gray Structures [pdf] (Manual Tracing for Hippocampus, Amygdala, Caudate, and Putamen)
- Tracing is done in a combination of the three orthogonal planes, as specified in the
detailed methods that follow. - Each region of interest was originally defined in the right hemisphere. The labels
were then reflected onto the left hemisphere and all borders checked and adjusted
manually when necessary. - For the initial parcellation, the user used the “paint over function” of IRIS/SNAP on
the T1 template of the atlas.
Regional and Lobe Parcellation Rhesus Monkey Brain Atlas [pdf] (Manual Tracing for Parcellation Template)
- Traces are performed in a systematic order they, allowing the more easily defined
regions to provide borders for the more difficult regions - Many parts of the protocol instruct the user to trace to or from the “depth” of a sulcus.
The “depth” of a sulcus refers to the gray matter/white matter border within the
sulcus. - Tracing is done in a combination of the three orthogonal planes, as specified in the
detailed methods that follow. - Each region of interest was originally defined in the right hemisphere. The labels
were then reflected onto the left hemisphere and all borders checked and adjusted
manually when necessary. - For the initial parcellation, the user used the “paint over function” of IRIS/SNAP
painting over label 1 and label 2 (GM and WM) of the hard tissue segmentation. The
resulting labels were then dilated to fill the entire brain space.
Structural MRI Quality Control Manual [pdf]
- This document provides information about how structural MRI T1w and T2w data is scored for its quality with respect to the presence of artifacts etc.
Infant Multi-Atlas Hippocampus and Amygdala Segmentation Information [pdf]
- This document discusses the AutoSeg based multi-atlas hippocampus and amygdala segmentation, followed by manual correction of the automatic segmentation.