Re: RF bias correction with mri_convert
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
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
Re: RF bias correction with mri_convert
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
Re: RF bias correction with mri_convert
Hi Bruce, et al, The Markov random field approach with FSL FAST is intensive (~ 2000 sec on Athlon 1700, 1Gb PC2700 on VIA KT333A) and the results appear to be good. Of course, it could be better to measure the quantity on the scanner. Would this approach require access and modification of the kspace images before reconstruction? Naturally we could all rest easily if the scanner engineering and signal processing took care of the problem ;-) We don't have a research scanner and any access to any of that :-( It would be nice to evaluate this latter physical solution with that from FAST. Thanks for clarifying the mri_normalize process. It will be interesting, although overkill, to see what happens when FreeSurfer is fed one of the volumes after RF correction with FAST. In particular, whether it will improve the segmentation any. Another interesting experiment might be to segment the WM with freesurfer and use that volume as a prior input to FAST. Again, overkill, but anything that could improve the automation of the first segmentation stage might decrease the latter manual editing. The cost is the extra processing overheads. Yes, there is some other work to be done on just the RF bias corrected volume. Cheers, Darren - 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
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
Re: RF bias correction with mri_convert
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
Re: RF bias correction with mri_convert
Hi Anders, Many thanks for this reply. We have been grappling with the non-linearity on our new Sonata systems, and will face the same hurdle with our 4T (Sonata gradients). Would it be possible to continue the discussion off-list about your correction procedure and how it is implemented in mri_convert? I also have access to a just-installed GE twinspeed system and would be happy to help in acquiring data with your phantom if you are unable to get the information from GE. regards, Greig On Friday, August 30, 2002, at 11:05 AM, Anders M. Dale wrote: 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 -- 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
