FW: [Eeglablist] fMRI artifact removal

[Yuko Yotsumoto]

Hi all,

Thank you very much for your advice and comments.
I've been talking to the tech people in my institution. Though we are 
still working on the technical details, we will probably be able to 
increase the sampling rates. I'll give an update if I can get EPI noise 
removed with different sampling rates.

Yuko Yotsumoto, Ph.D.
yuko at nmr.mgh.harvard.edu

Rami K. Niazy wrote:

> Hi All
> 
> For the fmrib plug-in, the sampling requirement is that you sample high 
> enough so that you do not have any aliasing in the data.  So that 
> depends on what filters your hardware has.  As a minimum, your hardware 
> should completely remove any frequencies above 400Hz or so to avoid 
> aliasing at 1kHz (theoretically, you should always sample at twice the 
> highest frequency in your data.  Practically, that should be 3-4 times 
> the highest freq.) 
> 
> Negishi et. al. (2004) applied similar techniques to those used in the 
> fmrib plug-in to data sampled at 1kHz and had good results.  We have 
> tried the fmrib plug-in on data collected at 1kHz and had really bad 
> results because high frequencies were aliasing.   At those low sampling 
> frequencies (1kHz - 2kHz), even though you avoid aliasing, you get some 
> shape differences in the artifact as Marcel has pointed out.  However, 
> our program is designed to approximate these differences and deal with 
> them so that you don't have to sample at 5kHz.  You just need to avoid 
> aliasing.
> 
> I hope that helps.
> 
> Regards,
> 
> Rami
> 
> Yuko Yotsumoto wrote:
> 
> 
>>Hi Marcel,
>>
>>According to their publication and web page, fMRIb plug-in works with 
>>as low as 2048 Hz sampling rate, which I think makes this plug-in very
> 
> 
>>valuable.
>>
>>But 957 Hz is probably too low... I am wondering if anybody knows the 
>>minimum requirement for sampling rate to apply fMRIb.
>>
>>Thanks,
>>Yuko
>>
>>Marcel Bastiaansen wrote:
>>
>>
>>>Dear Yuko,
>>>
>>>I have no experience with the fMRIb tool, but:
>>>
>>>It is my experience that everything below 1 KHz is way too low to 
>>>adequately sample the gradient artefacts produced by the EPI
> 
> sequence.
> 
>>>This will result in a shape of the gradient artefact that varies from
> 
> 
>>>volume to volume. This makes it impossible to compute anaverage 
>>>gradient artefact for the subtraction.
>>>
>>>You should sample at 5 KHz or higher to get rid of this problem.
>>>
>>>Kindly,
>>>Marcel Bastiaansen
>>>
>>>Yuko Yotsumoto wrote:
>>>
>>>
>>>>Hi all,
>>>>
>>>>I have EEG data recorded in the fMRI scanner.
>>>>Our EEGs were recorded with 957 Hz, while fMRI was operating at 4TR 
>>>>with 35 slices. Recording time was about 160 sec. Trigger signals 
>>>>were obtained at every image acquisition (=35 triggers for 4 TR).
>>>>
>>>>I'm trying to remove EPI noise artifacts with fMRIb plug-in, but 
>>>>have been unable to get clean results.
>>>>
>>>>With fMRIb plug-in, I used parameter sets such as follows.
>>>>
>>>>Low-pass filter cut off : 30
>>>>Interpolation folds : 21
>>>>Artifact-timing event : slice
>>>>ANC : on
>>>>Correct for missing triggers : off
>>>>Relative trigger location : 0
>>>># of residuals PC to remove : auto
>>>>
>>>>I am wondering if our sampling rate of 957 Hz might not be high 
>>>>enough to use fMRIb plug-in. Have anybody in this mailing list tried
> 
> 
>>>>this plug in with a similar sampling rate? Did it work?
>>>>
>>>>Thanks!
>>>>
>>>>Yuko
>>>>
>>>>
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>>>
>>
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> 
>