Hi - yes, we don't use the SUSAN nonlinear spatial filtering for the
FMRI preprocessing, so yes, you're best off just using the standard
linear filtering in ip. (We use SUSAN for nonlinear smoothing of the
autocorrelation estimation within the FILM timeseries whitening, but
this isn't what you're considering here.) So yes, I would just stick
with ip.
Cheers, Steve.
On 25 Oct 2006, at 10:47, Mareike Menz wrote:
> Hi,
>
> thank you for your quick answer. I started using ip for temporal
> filtering, esp. removing low drifts from the signal. I discovered
> that I can also apply spatial filtering using ip. The advantages
> are obvious to me - it is one step instead of two (using ip and
> susan_smooth) and it doesn`t need a change of magnitude of numbers
> (the 16bit integer issue in susan_smooth).
> So the question is basically about the linear Gaussian filtering
> and the lowpass median filtering - what do I lose by not using susan?
> I guess that can`t be answered in general but only for my data.
> That`s why I would like to read more about way the ip-filtering
> (esp. spatial) works, to understand what is doing what.
>
> I hope I was more precise this time...
>
> Mareike
>
>
>
> Steve Smith wrote:
>> Hi,
>> Yes, susan_smooth is nonlinear spatial smoothing, ip contains
>> various options, including lineas Gaussian smoothing, temporal
>> filtering and intensity normalisation.
>> Without knowing what context you are asking about it's hard to
>> answer your question - are you talking about smoothing of FMRI data?
>> Cheers.
>> On 24 Oct 2006, at 15:53, Mareike Menz wrote:
>>> Dear FSLers,
>>>
>>> I wonder about about the algorithm ip is using. As far as I
>>> understood it is different from susan_smooth - am I right about
>>> that?
>>> I also read about a difference between FSL and SPM in regard to
>>> smoothing/filtering.
>>>
>>> Maybe you could give me a hint, where to look for information?
>>> Is there any reference you could give to me or a technical report
>>> I could read? In case it is the susan-paper I`ve got it.
>>>
>>> Thank you in advance,
>>>
>>> greetings from Hamburg,
>>> Mareike
>>>
>>>
>>> --
>>> Mareike Menz
>>> NeuroImage Nord Lübeck
>>> University Medical Center Hamburg-Eppendorf, Bldg. S10
>>> Martinistr. 52
>>> 20246 Hamburg
>>> Germany
>>>
>>> +49 40 42803 3683
>>> [log in to unmask]
>>>
>>> --
>>>
>>> () ascii ribbon campaign
>>> /\ - against html mail
>> ---------------------------------------------------------------------
>> ------
>> 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
>> ---------------------------------------------------------------------
>> ------
>
> --
>
> Mareike Menz
> NeuroImage Nord Lübeck
> University Medical Center Hamburg-Eppendorf, Bldg. S10
> Martinistr. 52
> 20246 Hamburg
> Germany
>
> +49 40 42803 3683
> [log in to unmask]
>
> --
>
> () ascii ribbon campaign
> /\ - against html mail
------------------------------------------------------------------------
---
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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