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
