Open-Source frameworks for medical imaging

C++ frameworks are great to develop new methods from other previously coded methods. Here are some great frameworks for medical imaging:

ITK Insight Segmentation and Registration Toolkit http://www.itk.org/
As the name states, it is great for segmentation and registration, but also has filters, statistics...

STIR Software for Tomographic Image Reconstruction http://stir.sourceforge.net/
It is a open-source framework to reconstruct data for nuclear medicine.

ROOT Rapid Object Oriented  Data Framework http://root.cern.ch/
It is one of the major open source codes ever developed for Physics, so it is great to use in medical physics oriented medical imaging.

XIP eXtensible Imaging Platform   http://www.openxip.org/
https://wiki.nci.nih.gov/display/XIP/eXtensible+Imaging+Platform+-+XIP
A platform design for rapid development of medical applications including DICOM tools, renders...

MITK Medical Imaging Toolkit http://www.mitk.org/
A framework which comprises ITK and VTK, a visualization toolkit.

A complete list with more frameworks:
http://www0.cs.ucl.ac.uk/opensource_mia_ws_2012/links.html

Teaching MRI

Teaching MRI is a hard task, specially if the students don't have a strong physics background. Three of my favorite resources (and free) to use in classes are:

MRI online course: http://www.imaios.com/en/e-Courses/e-MRI
This online course has great animations to explain concepts and brief explanations. I think some of the animations are very helpful to explain details to students. You have to create an account to see the animations properly, but this requires little effort. 

Virtual MRI (VMRI): http://www.iftm.de/elearning/vmri/idx_vmri.htm
This program can be easily run in your computer and gives a good idea about parameters for several sequences (Spin-Echo, Gradient-Echo, Inversion Recovery, Fast Spin-Echo), such as TR, TE, TI and ETL. Furthermore, it shows the k-space of the images and allows us to manipulate it and see the effect. Other image quality parameters can also be changed: FOV, pixel size, ... I strongly recommend this for computer classes where students have to apply their knowledge.

OSIRIX DICOM database: http://www.osirix-viewer.com/datasets/
This database contains several MRI datasets acquired for different regions (with and without pathology) and with different sequences. I usually don't use OSIRIX, because I don't have MacOS... I use one of the free visualization programs I referred in this post.

TED talk about medical data explosion

Here is an interesting talk which tackles a lot of topics: CT, GPU, autopsies, animal imaging, fMRI...

Free Medical Imaging Visualization Sofware

If you ever worked with medical images, you know there is a confusion of data formats and programs to visualize images. It is true that the DICOM standard helped a little bit, but only a little bit. Interfile, Analyze, NIFTI are other image formats widely used. And probably, you don't want to spend money on programs to visualize medical images. Manufacturers have the possibility to burn a CD with your images and those CD's bring a visualization software to work with. Most health providers will give you a CD to take to your doctor.

Siemens offers the program Syngo fastView free download. This program helps you to visualize images and it is a very basic version of the hospital workstations. The good thing is that you can open DICOM images from other manufacturers such as Philips and GE (I personally have tried GE images).

If you are an open-source fan and/or have images which are not DICOM, there are several programs. I have experienced several of them and I will tell you about my favorite: AMIDE. 4 main reasons why I like this software: easy to install in any platform Linux, Windows and Macintosh, is able to save jpg for your documents, deals very well with several formats and it is possible to read images which are not any of the standard formats if you know the data details.



 Links:
Philips DICOM viewer
http://clinical.netforum.healthcare.philips.com/us_en/Explore/Clinical-News/MRI/Philips-DICOM-Viewer-download
Understanding and Using DICOM
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC61235/