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Lythgoe, David Mark Jenkinson thank you very much. Shiliang 2008/4/16, Mark Jenkinson <[log in to unmask]>: > > Dear Shiliang, > > You are right that there are many ways of dealing with signal loss at the > acquisition level. > There is no "software" that can "solve" it at the post-processing level > though. We have > some things implemented to try and reduce the effects of signal loss on > things like > registration, but they never restore signal. > > So what you need to do is explore the various acquisition options for > reducing signal loss. > Thinner slices can help a lot, and so can slice-dependent z-shimming, to a > lesser extent, if > you can get it implemented. In order to cope with increasing TR you could > consider trying > parallel acquisition acceleration to get your TR down again, although it > comes at the price of > some SNR reduction. Still, it sounds like you have found most of the > appropriate methods. > > I just wanted to say that I completely agree with David's earlier reply, > and to clarify that this > is really an acquisition issue and not one that FSL can deal with in > post-processing. > > All the best, > Mark > > > > On 15 Apr 2008, at 14:28, qiang wang wrote: > > > Hi Dave > > Thank you for your reply. But I found some papers on recovering > > susceptibility-induced signal losses. > > > > some authors have reported methods for recovering > > susceptibility-induced magnetic field gradient (SFG)-induced signal losses. > > The simplest method uses thinner slices to reduce the field change across a > > slice (1). However, this method reduces both the signal-to-noise ratio (SNR) > > and the spatial coverage per unit of time. Another method (2每4) effectively > > compensates for field inhomogeneities > > using multiple refocusing gradients. However, in practice, many > > repetitions are needed to sum up to a uniform image. This disadvantage > > limits its value in fMRI experiments. Some methods using high-order field > > compensation (5,6) and a two-shot technique (7,8) were more efficient but > > the repetition time (TR) was still doubled. > > > > > > 1. Young IR, Cox IJ, Bryant DJ, Bydder GM. The benefits of increasing > > spatial resolution as a means of reducing artifacts due to field > > inhomogeneities. Magn Reson Imaging 1988;6:585每590. > > 2. Frahm J, Merboldt KD, Hanicke W. Direct FLASH MR imaging of magnetic > > field inhomogeneities by gradient compensation. Magn Reson Med > > 1988;6:474每480. > > 3. Ordidge RJ, Deniau JC, Knight RA, Helpern JA. Assessment of relative > > brain iron concentrations using T2-weighted and T2*- weighted MRI at 3 > > Tesla. Magn Reson Med 1994;32:335每341. > > 4. Constable RT. Functional MR imaging using gradient-echo echoplanar > > imaging in the presence of large static field inhomogeneities. J Magn Reson > > Imaging 1995;5:746每752. > > 5. Cho ZM, Ro YM. Reduction of susceptibility artifact in gradientecho > > imaging. Magn Reson Med 1992;23:193每196. > > 6. Glover G, Lai S. Reduction of susceptibility effects in BOLD fMRI > > using tailored RF pulses. In: Proceedings of the 6th Annual Meeting of > > ISMRM, Sydney, Australia, 1998. p. 298. > > 7. Chen NK, Wyrwicz AM. Removal of intravoxel dephasing artifact in > > gradient-echo images using a field-map based RF refocusing technique. Magn > > Reson Med 1999;42:807每812. > > 8. Mao J, Song AW. Intravoxel rephasing of spins dephased by > > susceptibility effect for EPI sequences. In: Proceedings of the 7th Annual > > Meeting of ISMRM, Philadelphia, PA, USA, 1999. p. 1982. > > > > So I think there are many people do this work. Am I right? > > Shiliang > > > > > > 2008/4/14, Lythgoe, David <[log in to unmask]>: Hi Shiliang, > > > > The best software to use is the pulse sequence on your scanner. If you > > reduce the slice thickness, you'll reduce the through-plane de-phasing that > > causes most of the signal loss. If you increase the matrix size, you'll also > > reduce signal losses due to in-plane echo-shifting. > > If that solution isn't available, sigloss in FSL can provide an estimate > > of the signal loss, which can then be used to "correct" the signal. You'll > > also need a field map. One problem with this is it locally increases the > > noise. Also, in some regions the signal loss is so severe, any correction > > would be completely meaningless. Finally, I haven't used sigloss directly > > for some time, but I found it underestimates susceptibility-induced signal > > losses. In fact, I would advise against attempting to correct for lost > > signal using post-processing. Others may disagree. > > > > > > Dave > > > > > > > > > > > > -----Original Message----- > > From: FSL - FMRIB's Software Library on behalf of qiang wang > > Sent: Mon 14/04/2008 15:03 > > To: [log in to unmask] > > Subject: [FSL] Which software can solve the problem of > > susceptibility-induced signal losses in EPI images > > > > Dear every one > > > > I want to solve the susceptibility-induced signal losses in EPI images. > > Who > > can tell me which software can solve this problem? Thank you. > > > > Best wishes > > > > Shiliang > > > >