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FSL  May 2007

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Subject:

Re: Denoising 0.5 Hz scanner artefact

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 19 May 2007 08:42:16 +0200

Content-Type:

text/plain

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text/plain (64 lines)

Hi - it's easy to add confound EVs (covariates) in FEAT which would  
be equivalent to what you're doing in SPM - does this not do what you  
want?
Cheers.


On 18 May 2007, at 23:27, Rutger Goekoop wrote:

> Dear all,
>
> For some yet unexplained reason, a 0.5 Hz scanner artefact appears  
> in our 800
> volume PRESTO SENSE timeseries (TR 0.609). This noise sums nearly  
> linearly on
> top of existing BOLD signal intensity. Analysis shows that it can be
> eliminated during postprocessing using user-specified regressors in  
> SPM5
> (with delta functions every 4th scan) as follows:
>
> Regressor1:
> 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 ... etc: complete 800 volumes.
> Regressor2:
> 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 ... etc: complete 800 volumes.
> Regressor3:
> 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 ... etc: complete 800 volumes.
>
> This yields 3 PE images for these 3 regressors with almost 100% noise
> elimination with good residual SD.
>
> Since I want to use MELODIC for further study of these data (and  
> since I'm
> forever hooked to FSL), I'd like to do something similar in FSL. I  
> tried
> MELODIC denoising, however MELODIC does not find the relevant  
> components.
> Instead, nearly all components are contaminated with the 0.5 Hz  
> artefact
> (possibly because of its regular nature?). Thus, I think I may  
> first need to
> do a model-based analysis in all individuals (as in SPM5, see  
> above) using
> custom EVs with delta functions, and then somehow filter out the  
> beta images
> from the filtered_func_data (using avwmaths?). Or is there perhaps  
> a more
> sound way of dealing with this problem?
>
> Any help would be greatly appreciated,
>
> Cheers,
>
> Rutger Goekoop.


------------------------------------------------------------------------ 
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------ 
---

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