We have developed robust QSM software for both clinicians and researchers. For clinicians interested in using QSM in their daily practices, we present an automated QSM workflow that can be implemented across major MRI manufacturers at both 1.5 and 3T. QSM is automatically reconstructed and available for viewing at the end of each patient MRI session. For researchers interested in further developing QSM algorithms, we present MATLAB tools and source codes for the core Bayesian QSM algorithm, along with implementation for nonlinear field estimation, field unwrapping and background field removal. A GUI tool is provided and demonstrated.
We have established automated QSM to enable utilization in clinical practice. After a multi echo 3D gradient echo (GRE) sequence is completed, the DICOM images (both magnitude and phase, or real and imaginary) are transferred immediately to a dedicated desktop computer with no human intervention (GE) or with a click by a technician at the scanner console (Siemens and Philips, we are working on eliminating this click). Upon receiving data, the computer automatically performs QSM reconstruction. As the reconstruction finishes (in 8 min), the computer automatically transfers QSM images (DICOM format) back to the scanner console or PACS system. Meanwhile, all images are archived in a backup drive which is connected to the reconstruction server. The entire process takes about 20 min on average at Cornell, so QSM images are available by the end of a patient MRI session. This automated QSM streamline has been distributed and installed on multiple sites.
Phase image data need to be properly acquired and saved on a MR scanner for reliable QSM. We recommend the following brain protocol using 3D multi-echo GRE sequence with outcome of DICOM images for magnitude/phase or real/imaginary channels: flow compensation on, 1st TE ~ 3 msec, TE spacing = 3 msec, # of TEs = 6~12, TR = 50~60 msec, flip angle = 20, bandwidth 400 Hz/pixel, FOV = 24 cm, slice thickness = 1~2 mm, matrix size = 400x300x88~176, head surface coil array (8~32 channels) with acceleration factor = 2. Total scan time is about 6~12 minutes and dependent on the prescribed resolution and image volume.
We recommend clinicians to work with manufacturers and physicists in setting up automated QSM. There are potential issues in saving proper phase image data, which are related to the manufacturer-specific implementations of the GRE sequence. The magnetic field determination from phase data depends on readout gradient polarity in multiecho GRE. Any phase filter needs to be turned off, and some manufacturers may have echo-dependent phase modulation that needs to be turned off or removed during recon. Because phase data has traditionally been discarded, older software versions of MRI systems may have phase bugs, which may require a software upgrade or a substantial effort to re-engineer proper phase extraction from coil array.
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