Greig is correct. The --unwarp-gradient-nonlinearity option corrects for the 3-D image distortions caused by departures from linearity in the magnetic fields produced by the x-, y- and z- gradient coils. These distortion patterns are specific to each scanner/gradient model (e.g., Sonata, Quantum, Allegra for Siemens scanners; SX, SmartSpeed, EchoSpeed, etc, for General Electric scanners).
At present, we have implemented corrections for Siemens Sonata/Trio and Allegra gradients, and plan to add other models as we obtain the neccessary calibration info (from scans of a specially designed distortion phantom, or, ideally, in the form of spherical harmonic coefficients for each gradient model provided by the scanner manufacturer.) Cheers, -Anders . -- Anders M. Dale email: [EMAIL PROTECTED] MGH NMR Center tel:(617)-724-9771 149 13th St., Rm. 2301 fax:(617)-726-7422 Charlestown, MA 02129 a.. SmartSpeed= 23mT/m a.. HighSpeed Plus / EchoSpeed Plus = 33 mT/m. ----- Original Message ----- From: "Greig de Zubicaray" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Thursday, August 29, 2002 8:16 PM Subject: Re: RF bias correction with mri_convert > Hi Darren, > > I think you'll find that this option refers to the fact that the > gradients in many of the latest generation MRI systems from several > manufacturers are not exactly linear, particularly in z. Obviously, this > has implications for the imaging experiments performed on them, > particularly if you don't use the centre of the magnet! The MGH > researchers very nicely submitted an abstract to HBM2001 at Brighton > documenting these non-linearities in their GE and Siemens systems. See: > > Wald, L., Schmitt, F., Dale, A. (2001). Systematic spatial distortion > due to gradient non-linearities. Neuroimage, 13(6), S50. > > I would also be interested to hear what the unwarping procedure entails? > > regards, > > Greig > > > > > > On Friday, August 30, 2002, at 08:54 AM, Darren Weber wrote: > > > > > I am referring to a command line option to mri_convert: > > > > --unwarp-gradient-nonlinearity ... > > > > > > > > > > ----- Original Message ----- > > From: "Bruce Fischl" <[EMAIL PROTECTED]> > > To: <[EMAIL PROTECTED]> > > Sent: Thursday, August 29, 2002 9:30 PM > > Subject: Re: RF bias correction with mri_convert > > > > > >> p.s. what we do is not really bias field estimation/correction, but > >> something much more aggressive, really a pre-segmentation, which > >> accounts > >> for bias fields as well as tissue inhomogeneity. If what you want is > > really > >> the bias field for some other purpose, you're probably better of using > >> the > >> EM stuff from the FSL (unless you can measure it directly with your > >> scanner, which is the best solution!). > >> > >> Bruce > >> > >> On Thu, 29 Aug 2002, Stephen Smith wrote: > >> > >>> > >>> Hi - no, it doesn't - that is part of the initial freesurfer > >>> processing > >>> (which estimates white matter and then estimates bias field on the > >>> basis > >>> of white matter points), not the format conversion. > >>> > >>> ttfn, Steve. > >>> > >>> On Thu, 29 Aug 2002, Darren Weber wrote: > >>> > >>>> > >>>> Dear Bruce et al, > >>>> > >>>> does mri_convert automatically apply RF bias field > > estimation/correction? > >>>> If it can do the RF bias correction, what is the best command line > > option > >>>> for this? > >>>> > >>>> Take care, Darren > >>>> > >>>> > >>>> -- > >>>> Darren Weber, PhD Student > >>>> Cognitive Neuroscience, School of Psychology > >>>> Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust. > >>>> Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877 > >>>> http://203.3.164.46/~dlw/homepages/index.html > >>>> > >>>> > >>>> > >>> > >>> Stephen M. Smith > >>> Head of Image Analysis, FMRIB > >>> > >>> Oxford University Centre for Functional MRI of the Brain > >>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > >>> +44 (0) 1865 222726 (fax 222717) > >>> > >>> [EMAIL PROTECTED] http://www.fmrib.ox.ac.uk/~steve > >>> > >> > >> > > > > > > > -- > Dr Greig de Zubicaray > Research Fellow > Centre for Magnetic Resonance > The University of Queensland, Brisbane, QLD 4072, Australia > > Tel: +617 3365 4250 [direct] > +617 3365 4100 [reception] > Fax: +617 3365 3833
