[Mrtrix-discussion] calculating recovered HARDI / residuals

[Jeurissen Ben]

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> 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
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-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078

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