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 (2–4) 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;6:585–590.
> 2. Frahm J, Merboldt KD, Hanicke W. Direct FLASH MR imaging of  
> magnetic field inhomogeneities by gradient compensation. Magn Reson  
> Med 1988;6:474–480.
> 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;32:335–341.
> 4. Constable RT. Functional MR imaging using gradient-echo  
> echoplanar imaging in the presence of large static field  
> inhomogeneities. J Magn Reson Imaging 1995;5:746–752.
> 5. Cho ZM, Ro YM. Reduction of susceptibility artifact in  
> gradientecho imaging. Magn Reson Med 1992;23:193–196.
> 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;42:807–812.
> 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
>