Obtaining Scan Data From IRC Siemens MRI Scanners

Purpose

To provide a recommended best practice for obtaining data from the IRC's Siemens MRI scanners

Introduction

There are several methods users may employ to get their data from the IRC's MRI scanners, but there is only one method that is endorsed and recommended by the IRC.

Several research groups prefer to bring a USB drive with them and transfer their data to that drive at the end of their scan. But there are several drawbacks to using USB drives, and they don't end with risk to the group using them. USB drives suffer from the following problems:

• They are prone to read/write errors.
• Their connectors are not built for many insertions and removals and become worn quickly.
• The USB ports on the host computer are also not designed for repeated use and become worn, and damage to those causes problems for everyone.
• USB drives are prone to data corruption when removed without properly ejecting, which is quite common.
• Exporting data to a USB drive does NOT simply copy files from the host. It collects header information and image data from three different physical hard drives on the host, and builds DICOM files on the fly. This is CPU intensive, and it slows down the host to the point that the next user is frequently affected.
• Their small size makes loss a real concern which is realized almost weekly in the control room when IRC staff finds left drives.

For these reasons, the IRC discourages USB drives. And, for some of the same reasons and additionally owing to the length of time it takes to burn a DVD, the IRC also discourages use of DVDs for anything but providing anatomical images to the research subjects as a souvenir of sorts.

OsiriX Access

The IRC operates an OsiriX instance that accepts data from the IRC's scanners at the end of every single scan. Those data are instantaneously available from the OsiriX web interface.

The web portal is available at this URL: https://sweetn.irc.utexas.edu:3333/

Login credentials are issued to each group and managed by the PI. The IRC can not give you access to your PI's data. If you need access to OsiriX, ask your PI to retrieve their credentials from Stache and give them to you.

Using OsiriX

The interface is fairly self-explanatory, but a few pointers are provided on the OsiriX T&T page. 

There is one common complaint that some people have when using OsiriX, and that is when your data are downloaded in a zip file, all the DICOMs are organized in a single directory (folder) instead of sorted into individual directories named by the scan description. There are two ways to solve this issue. The first way is to use the MATLAB function splitSiemensScans.m provided on the IRC's GitHub repository. This function sorts the scans exactly the same way the host computer does when it exports them to a USB drive. The second method doesn't require the use of MATLAB and is slightly faster. DSI Studio is a package that is designed for the processing of diffusion data, but it includes a helpful tool that sorts the files the same way. When you start DSI Studio, click the "Batch Processing" tab on the left of the window. There are two tools named "Rename DICOM files," and the second one (that accepts a directory full of unsorted DICOMs) will sort them perfectly.