B0 and eddy current correction code for diffusion MRI
Figure: A) DTI dataset containing one base image and six diffusion weighted images. B) DTI dataset after geometric correction using B0 field map only. C) DTI dataset after the full correction procedure using B0 field map and eddy current gradient field maps. D) The difference images between C (full correction) and B (B0 correction only). The corresponding shearing and scaling effects due to eddy currents are indicated by arrows. The first column shows the B0 field map.
Overview
- Diffusion tensor imaging (DTI) has seen increased usage in clinical and
basic science research in the past decade. By assessing the water diffusion
anisotropy within the biological tissue, e.g. brain, researchers can infer
different fiber structures important for neural pathways. A typical DTI dataset
contains at least one base image and six diffusion weighted images along non-collinear
encoding directions. The resultant images can then be combined to derive the
three principle axes of the diffusion tensor and their respective cross terms,
which can in turn be used to compute fraction anisotropy (FA) maps, apparent
diffusion coefficient (ADC) maps, and to construct axonal fibers.
- The above operations all assume that DTI images along different encoding
directions for the same brain register to each other without spatial distortions.
This assumption is general false, as the large diffusion weighting gradients
would usually induce eddy currents to generate encoding-direction dependent
field gradients, leading to mis-registration within the DTI dataset. Traditional
methods for correcting magnetic field induced distortions do not usually take
into account these direction-dependent eddy currents unique for DTI, and they
are usually time consuming because multiple phase images need to be acquired.
- The theory and implementation of a fast, efficient and effective method
to correct for the main field and eddy current-induced direction-dependent
distortions for DTI images under a unified frame to facilitate the daily practice
of DTI acquisitions have been reported (see References below).
- Here we disseminate the software used in the published work, excecutable and source code.
Implementation on GE Horizon
See References below.
Implementation on Siemens Trio
- The ep2d_difm pulse sequence is an adaptation of the Siemens pulse sequence
ep2d_diff. The new sequence maintains the same functionality as its predecessor.
Additional functionality was added to allow users to subsequently acquire
B0 and/or eddy current multi-echo phase maps from the prescribed slice locations
in an additional series.
- A new task card has been added to the console, under Sequence -> Special,
which contains the two controls for acquiring field maps. An On/Off widget
and a widget for entering the number of echoes to acquire in the EPI pulse
train for each phase encode.
- Acquired files are fully compatible to the distributed software for image
distortion correction.
- The pulse sequence will be distributed using the standard Siemens C2P scheme. Paperwork for the C2P is in progress. Installation and usage literature will be developed and distributed as per usual for Siemens requirements.
User Manual
User Manual The distribution also includes a readme.htm file with use and installation instructions.
References
Bin Chen; Hua Guo; Allen W. Song. Fast Correction for Direction-Dependent Distortions in Diffusion Tensor Imaging Using Matched Magnetic Field Maps, NeuroImage (in press)
Technical Contact
Please email your comments to: Bin Chen