stnava / antstutorial

Guide to tutorial materials for ANTs/R

ANTsTutorial

Guide to tutorial materials for ANTs/R

Overview

The goal of this tutorial is to use ANTs and ANTsR to turn raw data into clean data.

We will focus on pediatric brain magnetic resonance images available in the PTBP and show how to:

• Organize and inspect the raw data and identify potential problem cases.

• Identify hypotheses and quantification targets, given our data.

• Develop a template construction procedure to address our hypotheses.

• Attach prior distributions to the template.

• Process the full data with ANTs pipelines.

• Extend the baseline processing to interpret auxiliary modalities.

• Perform univariate and multivariate statistical tests.

• Explore prediction algorithms based on imaging data.

Along the way, we will cover theoretical foundations as well as practical insights arising from our experience with processing biological images numbering from the tens to tens of thousands.

Special sub-topics may include:

• Baby brain

• Multivariate neighborhood segmentation models

• Longitudinal processing

• Multivariate everything ...

• ASL processing

• Patch-based analyses for cross-modality inference ...

We will also entertain other requests.

Data sources

A complete multi-modality subject http://files.figshare.com/1701182/PEDS012_20131101.zip

PTBP demographics here

PTBP tutorial data [here](https://www.dropbox.com/s/5p0vlx8en9uzbge/ ants_tutorial_data.zip?dl=1)

Elderly subject data here

Software dependencies

Core: ANTs, ITKR, ANTsR

Suggested: Camino, ITK-SNAP

The above tools depend on R, cmake and java.

Supported platforms include OSX and Linux variants.

These may work on windows but we do not regularly test there.

antstutorial's Issues

2D registration

Dear Ants community,

I have 200, 2D images and I want to do internal registration( registering all the images into one of the images to make sure they are aligned).I think only rigid registration should be ok.Can I do that with Ants?If yes could you please help me with the instruction?

Regards

*K* Easy Pieces: Adaptable tutorial content

Some topics - let's try to keep each topic to n slides. Let's call 10<=n<=20 for a start. If topics are too large, let's break them into smaller pieces. Might move some of this content to the wiki.

• antsRegistration
• Atropos
• JLF

*template construction will include JLF and above

• antsCorticalThickness will relate to all above
• Example data from PTBP
• ANTsR basics
• Visualization tools such as antsSurf and ITK-SNAP
• Multiple modality processing strategies as in PTBP and circularity paper
• Cerebral blood flow
• BOLD pre-processing: for rsf and task ... let's focus on pre-pro, deal less with statistics ... but we can make some graphs and some blobby overlays ...
• SCCAN and Eigenanatomy ....
• Here is some other information related to our existing / past ( disorganized / not well-integrated ) documentation / tutorial material at rubs.