Status: In production
The goal of this software is to provide a 3D correction of image distortions in MRI data due to non-linearity of the magnetic fields from the imaging gradient coils.
One of the challenges for a multi-site or longitudinal trial is to minimize image variations due to imaging gradient hardware. Imperfections in magnetic field gradient pulses can result in image warping and may limit the detection power of a study attempting to detect structural variations due to pathology. It has been shown that image distortions can significantly affect the quantitative measure of volume, shape, and boundary. The most common source of image distortion is imaging gradient non-linearity, which can distort the images not only in the in-plane directions, but also out of plane.
The Morphometry BIRN is making available a gradient non-linearity distortion correction algorithm, developed at the MGH and UCSD sites, that reduces image distortions and improves test-retest reproducibility of image intensity in multi-site structural MR data studies.
The manuscript from this work has been published:
Jovicich, J, Czanner, S, Greve, D, Haley, E, van der Kouwe, A, Gollub, R, Kennedy, D, Schmitt, F, Brown, G, Macfall, J, Fischl, B, Dale, A. Reliability in multi-site structural MRI studies: Effects of gradient non-linearity correction on phantom and human data. NeuroImage 30:436-443, 2005.
The gradient unwarping software package is available here.
The scripts in this package use spherical harmonics information specific for each scanner gradient set. The tables of spherical harmonics must be obtained by each user from their scanner manufacturer. The scripts do not provide spherical harmonic information in any form (neither the spherical harmonics themselves nor the calculated displacement file) because this is proprietary information. Currently, the user must contact the vendor to get the gradient spherical harmonics information and then use BIRN scripts to create a displacement table (which is used by the image correction software).
The mBIRN makes available to the public a phantom specifically designed to measure the image distortions due to gradient non-linearities.
The gradients supported by this software include:
- Cardiac Resonator Module (CRM) gradient coils from GE Medical Systems (maximum strength = 40 mT/m, slew rate = 150 T/m/s);
- Brain Resonator Module (BRM) gradient coils from GE Medical Systems (22 mT/m, 120 mT/m/ms);
- Sonata gradient coils from Siemens Medical Systems (40 mT/m, 200 T/m/s);
- Avanto gradient coils from Siemens Medical Systems
To use this tool: http://www.nitrc.org/projects/grad_unwarp
