![]() ![]() FSL has great tutorials and tools that help deal with EPI distortions using a field map that you should acquire in addition to your diffusion scan. An example of EPI distortions is shown in the image below. You can find more info on EPI distortions in this blog post. Remember to please direct software specific questions to their own respective forums or mail lists.ĮPI (aka field or B0-susceptibility) distortions are caused by magnetic field inhomogeneities, and are more obvious to spot then eddy currents. Please make sure to describe your question as clearly as possible. If you run into issues going through this tutorial please direct your questions to the diffusion imaging forum, where there will likely be someone able to help you out. Make sure you remove any non-brain tissues.Īt the end of the document you will find a pdf with the answers to the questions in this tutorial, although try to figure things out yourself as much as possible. It is important to deal with distortions common to diffusion images, like EPI and eddy currents.Ĥ. You will have to move the data off the scanner and convert it to a usable format.Ģ & 3. In order to get to tensor images there are a number of intermediate steps that are essential to go through:ġ. In this first tutorial the overall goal is to demonstrate how to convert raw diffusion data files to tensor images. Beyond that you can check out the post on diffusion imaging 101, and start perusing other posts on this website. Finally, this DTI tutorial assumes a basic understanding of diffusion MRI, if you would like to catch up on that first, you can go trough these slides that introduce this tutorial. If you would like some advanced tutorials that go into scripting in bash you can check out this linux tutorial, as scripting in linux will become an important skill when datasets get large. ![]() An example of linux tutorials can be found online, for example the " UNIX Tutorial for Beginners" contains explanations of basic commands commonly used to navigate the terminal. If you are not already, try to become comfortable in a linux environment. Most of the publicly available (and thus free) software tools used in neuro-imaging will only work in a bash terminal environment (linux or mac). ![]() These question will sometimes ask you to install software or download example data, you can find the example data for this tutorial here. There will be questions in each section to allow you to actively work with data and tools. As you get more versed with the different steps and software you will be able to try different packages and see which you prefer best. Always keep in mind that there are many ways of processing your data, and the examples used in this tutorial provide just one way of doing things. To make this process easier and help you get started with diffusion imaging analyses I put together this tutorial that will introduce you to the most important processing steps and tools. Starting out with data analysis often seems like a daunting task, as there are innumerable software packages with sometimes poor documentation. ![]()
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