[Mrtrix-discussion] calculating recovered HARDI / residuals

[Kerstin Pannek]

Hi Ben

very interesting work! I'd be really keen to try your method if you 
don't mind sharing your code. Thanks!

Cheers
Kerstin


Jeurissen Ben wrote:
>
> Hi Kerstin,
>
>  
>
> Based on my experience (simulations actually), I found that the 
> residuals from CSD generated signals **don’t** allow accurate variance 
> estimates with residual bootstrapping.
>
>  
>
> Calculating the residuals from the least square SH fit, however, 
> produced very accurate variance estimates (for details, see 
> http://www3.interscience.wiley.com/journal/123476777/abstract).
>
>  
>
> If you are interested, I can provide you with Matlab code that allows 
> you to use this method.
>
>  
>
> The problem with using the signal from CSD FOD’s is that it is not 
> clear how to correct for leverage (equation 8 in the mentioned paper), 
> since the CSD operation is iterative and uses the non-negativity 
> constraint. If you just leave out the leverage term in the residual 
> bootstrapping procedure, then your variance estimates will be biased 
> to a great extent. If I just use the leverage values from the last 
> iteration, the bias becomes less but is still much larger then when 
> residual bootstrapping with the SH model.
>
>  
>
> Cheers,
>
> Ben**
>
>  
>
>  
>
>  
>
> *From:* mrtrix-discussion-bounces at public.nitrc.org 
> [mailto:mrtrix-discussion-bounces at public.nitrc.org] *On Behalf Of 
> *Donald Tournier
> *Sent:* donderdag 10 juni 2010 4:01
> *To:* k.pannek1 at uq.edu.au
> *Cc:* mrtrix discussion
> *Subject:* Re: [Mrtrix-discussion] calculating recovered HARDI / residuals
>
>  
>
> Hi Kerstin,
>
>  
>
> There is no code to do that currently, but it really shouldn't be too 
> hard. The simplest thing to do would be to copy and modify 
> cmd/sdeconv.cpp (the simple linear spherical deconvolution), to 
> produce the modeled DW signals. You'll need to invert the operation, 
> so that the SH coefficients file is the input, and the DWI file is the 
> output. You can remove a bunch of options that you won't need (lmax, 
> mask, filter & normalise) and all the associated code that depends on 
> those options. You'll be determining lmax from the CSD file, 
> using DWI::SH::LforN (SH.dim(3)), and instead of converting from 
> amplitudes to SH, you'll be doing the opposite operation - at line 
> 213, use SHT.SH2A (sigs, res). There's obviously quite a lot more work 
> to it, but the rest should be *relatively* trivial...
>
>  
>
> Get in touch if you get stumped...
>
> Cheers, and good luck!
>
>  
>
> Donald.
>
>  
>
> On 10 June 2010 11:04, Kerstin Pannek <k.pannek1 at uq.edu.au 
> <mailto:k.pannek1 at uq.edu.au>> wrote:
>
> Hi
>
> I would like to calculate the residuals of my HARDI data for 
> bootstrapping.
> Is there a way in mrtrix to recover the HARDI signal from the csd, or 
> could you let me know how to bring csd, response and gradient 
> directions together to get the HARDI signal?
>
> Thanks
> Kerstin
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org <mailto: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 9496 4078
>