[Mrtrix-discussion] Re: Mrtrix-discussion Digest, Vol 43, Issue 12

Thu Aug 16 07:17:48 PDT 2012

Hi Donald, 
Thank you very much for your help!
For the number of directions, I understand that it's better to stay between 60 and 80 and repeat the measure. 
And for the voxel size, it will be difficult to go below 2mm isotropic with a bvalue of 3000...
Thank you very much for your advice about rician bias and motion correction. 
Cheers, 
Romain
On 15 août 2012, at 20:00, mrtrix-discussion-request at www.nitrc.org wrote:

> Send Mrtrix-discussion mailing list submissions to
> 	mrtrix-discussion at www.nitrc.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
> or, via email, send a message with subject or body 'help' to
> 	mrtrix-discussion-request at www.nitrc.org
> 
> You can reach the person managing the list at
> 	mrtrix-discussion-owner at www.nitrc.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Mrtrix-discussion digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: best parameter with a long-time scan? (Donald Tournier)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 15 Aug 2012 10:34:09 +1000
> From: Donald Tournier <d.tournier at brain.org.au>
> Subject: Re: [Mrtrix-discussion] best parameter with a long-time scan?
> To: romain quentin <rom.quentin at gmail.com>
> Cc: mrtrix-discussion at www.nitrc.org
> Message-ID:
> 	<CAPP9hqR3TH53MK4jJ7k6jGwq3YF4ic+8M8Pu9qaRC074x3+BMg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Romain,
> 
> In terms of the number of directions, I don't think it'll be worth
> increasing the number beyond around 60 - I had an ISMRM abstract about this
> a while back (which I'll hopefully get published at some point soon)
> showing that you really can't see much in the SH terms above lmax=8.
> There's just a suggestion of an lmax=10 term at b>=3000, but it'll be
> drowned in the noise for any realistic protocol. That mean you'll need at
> least 45 directions (for lmax=8), and I'd recommend going beyond that
> minimum number to make sure the problem is comfortably over-determined.
> This is particularly important if you're going to perform motion-correction
> (which you should given the length of your scan) with rotation of the
> gradient directions, a process that will tend to reduce the uniformity of
> your gradient directions. That said, you'll probably find it
> near-impossible to perform good motion correction - more on that later...
> You might want to push the number of directions beyond 66 if you really
> want to get the lmax=10 terms (maybe ~80 to make sure it's
> over-determined), but I'm not sure it'll necessarily make much of a
> difference. Otherwise, I'd recommend you repeat those directions, which at
> least gives you the potential to do something with the redundancy...
> 
> A bigger problem you'll face is the consequence of the low SNR you'll have
> given your small desired voxel size and higher b-value. While I'd consider
> that b-value to be optimal in terms of contrast-to-noise ratio, it does
> cause other problems when the SNR is low: Rician bias, and poor performance
> on just about any motion correction algorithm. The problem with the Rician
> bias is that even with a lot of averaging, the noise floor on magnitude
> data will push up the low signal intensities, and this tends to reduce the
> contrast between low SNR amplitudes. If you have a small voxel size (low
> SNR in each DW image), then the noise level will probably be of the same
> order as the DW signal, and this will tend to flatten out the angular
> contrast. The other problem is that this non-zero background signal will
> tend to introduce noisy peaks in the FODs, since the CSD process will
> interpret them as signal and try to fit lobes to match the noise - you'll
> probably see lots of noisy peaks in the ventricles for example. There have
> been a few methods proposed to rectify the Rician bias, and you may find
> that they can help, but I have no experience with this.
> 
> Motion correction is another problem in high b-value HARDI, because of the
> low SNR on the one hand, and because the contrast between the different
> images is further exaggerated, with makes life very difficult for the usual
> image matching metrics (mutual information, typically). In my experience,
> most methods currently available introduce more artefacts into the
> reconstruction than they solve. We had an abstract on a mask-based method
> to perform robust motion correction on high b-value data at this year's
> ISMRM (Dave Raffelt) and Jesper Andersson also had a method based on
> Gaussian processes. You might find that one or both of these approaches
> could be used, but as far as I know neither is currently available. We're
> planning on making the mask-based method available in a future version of
> MRtrix, but it's not ready yet...
> 
> One much easier option for motion correction when you're confident your
> subject won't move suddenly, is to intersperse b=0 images every ~10 DW
> images, so you can estimate the motion based on these b=0 images and
> interpolate the motion parameters to apply them to the DWIs. This is the
> approach I'd originally used for my 2004 spherical deconvolution paper,
> which also was a ~1h acquisition, and that worked pretty well. Not robust
> enough for patients though, they'll tend to move in jerks, which introduces
> higher frequencies in the motion than you can capture with the b=0 images,
> and also tends to corrupt the signal due to intra-volume mis-registration
> and signal dropout.
> 
> Hope that helps.
> Cheers,
> 
> Donald.
> 
> 
> On 14 August 2012 22:19, romain quentin <rom.quentin at gmail.com> wrote:
> 
>> Dear experts,
>> I'm using CSD from mrtrix with a diffusion sequence with b = 1500, 32
>> channels coil, 60 directions and isotropic 1.7mm voxels. This sequence
>> takes about 15 minutes.
>> I want to acquire a better diffusion sequence with more scanning time
>> (around 1 hour). I think to use b value = 3000 but i'm not sure about the
>> voxel size and numbers of directions.
>> Do you think it's better to do 4 x 60 directions, 2 x 120 or around 200
>> directions of diffusions?
>> And I know that reduces the voxel size is risky for the SNR but do you
>> think that I can keep a 1.7 isotropic regard to the time scanning (1 hour)?
>> Thank you very much for your help.
>> Best regards,
>> 
>> Romain QUENTIN
>> rom.quentin at gmail.com
>> 01 42 16 00 67
>> 06 80 33 15 74
>> 
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>> 
> 
> 
> 
> -- 
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20120815/3f302040/attachment-0001.html
> 
> ------------------------------
> 
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
> 
> 
> End of Mrtrix-discussion Digest, Vol 43, Issue 12
> *************************************************

Romain QUENTIN
rom.quentin at gmail.com
01 42 16 00 67
06 80 33 15 74