Research Specialist Training
1. Intro to Image Analysis slides
Check out a quick intro to RS-I duties here
2. Imaging Guides
Thoroughly read through the following guides. These were created by Mark Jenkinson, Thomas Okell, and Michael Chappell at the FMRIB Analysis Group at Oxford University. This group is responsible for the MRI image analysis toolbox called FSL, which you will use often as your time as an RS in our lab.
3. Papers
Read the following papers to orient yourself in the world of diffusion imaging.
4. LabNotebook, Supervisor Check-ins, and Weekly Meetings
As an RS, in addition to image analysis and data management, you also have a few administrative and logistics duties.
Each week, the lab meets on Thursdays at 2PM to discuss our projects, WIPs, ideas, problems, wins, and any other news that needs to be brought to the group. You will be expected to attend this each week and, eventually, occasionally present data yourself (don't worry, your supervisor will help you with this!)
During your training (the first 3-6 months of your time in the lab) you will have a weekly check-in with your supervisor in which you will go over the following form together:
You are expected to keep a lab notebook on LabArchives during your time in the lab. You can log into LabArchives here with your NetID and password. MUSC requires that the PI of the lab "owns" everyone's lab notebook. So Anya will make a lab notebook for you and then add you as an editor to that notebook. Once this happens, you will see a notebook with your name in this style: LAST,first. From there, you can create folders for different projects and pages within those folders for various pipelines and subprojects.
5. Workspace Setup
In order to get immerse yourself in command line interface, moving between programs and programming languages, and navigating the documentation and processes of the various open source software we use, you should seek out and install all of the necessary software yourself.
Though this is not an exhaustive list of all of the software you will ever use, download the following pieces of software:
Filezilla - an FTP software that allows us to access CBIHome (the repository where all of our MRI data is deposited immediately following a scan
bash unzip - a tool for use within a Mac or Linux Terminal to batch unzip folders or files
dicom-sort - a tool for use within a Mac or Linux Terminal to sort dicoms by sequence
MRIcron - a MRI nifti viewer that comes packaged along with dcm2niix, a tool for converting dicoms to niftis
Horos - a free tool for viewing and QCing dicoms
FSL - a large toolbox of many types of MRI data analysis tools
MRTrix3 - a large toolbox of many types of MRI data analysis tools
Python - a programming language used to write many tools we use in our lab, as well as with many useful MRI data analysis modules
PyDesigner - an in-house diffusion MRI preprocessing tool which performs a variety of image artifact correction sets as well as tensor estimation and parametric map calculation
MATLAB - a programming language and framework that is used primarily for a select few processes within the lab (namely Lesion Segmentation Tool (LST))
SPM - a toolbox similar to MRTrix3 and FSL that runs exclusively in MATLAB
LST - the Lesion Segmentation Tool, also used within MATLAB
Microsoft Office - you know what this is
6. Image Analysis - First Steps
Proceed to the dicoms page under the Image Analysis tab for a run down of MRI data management.
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