Hi Annelene,
I am not familiar with multi-segment EPI, but my guess is that you
should use a TR of 3 seconds.
Cheers,
Paul
On 02/01/2019, Annelene Gulden Dahl <[log in to unmask]> wrote:
> Great, thanks for your help!
> My sequence is a 2-segment EPI, so the (actual) TR is 1.5s, but the full
> volume TR is 3s (2x 1.5), which one is it that I should be using?
> Best, and happy new year,
>
> Annelene
>
>
>>-----Original Message-----
>>From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of
>>paul mccarthy
>>Sent: Sunday, December 30, 2018 6:54 PM
>>To: [log in to unmask]
>>Subject: Re: [FSL] How to filter out frequency identified in 'power spectra
>> 3'
>>window in FSLeyes
>>
>>Hi Annelene,
>>
>>The units along the X-axis are the signal frequency. You can use the -bptf
>>option to fslmaths to apply a band-pass filter. You need to specify the
>> high-
>>and low-pass frequencies as sigma values in volumes.
>>You can convert from frequency to sigma (in volumes) using the following
>>formula:
>>
>>sigma_vols = 1.0 / (2.0 * freq * TR)
>>
>>So if, for example, your data has a TR of 2 seconds, and you want to filter
>> out
>>frequences in the range 0.09-0.11Hz, you would use the following sigma
>>values:
>>
>>sigma_lp = 1.0 / (2.0 * 0.09 * 2.0) = 2.7778 sigma_hp = 1.0 / (2.0 * 0.11 *
>> 2.0) =
>>2.2727
>>
>>i.e.
>> fslmaths <input> -bptf 2.2727 2.7778 <output>
>>
>>However, the low-pass filter has a very slow roll-off, so you may need to
>>experiment a little with the low-pass sigma to get the results you want.
>> Also
>>note that you may wish to de-/re-mean your data before/after applying the
>>filter.
>>
>>See these posts for more information:
>> - https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;9ffadc97.1109
>> - https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;36bcf0ce.1709
>> - https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;c65efaab.1312
>>
>>Cheers,
>>
>>Paul
>>
>>
>>
>>
>>
>>
>>On 30/12/2018, Annelene Dahl <[log in to unmask]> wrote:
>>> Hi!
>>>
>>> I have discovered an artifact that keeps appearing in the resting
>>> state raw data in all my subjects, and using FSL eyes, it seems from
>>> the 'Power Spectra 3' window that it has a very specific frequency,
>>> which extends over multiple components seen with ICA. I am attaching a
>>> screenshot of the FSL/Melodic view to make it clearer.
>>>
>>> I would like to try to filter out this frequency, and in doing so I
>>> have two
>>> questions:
>>>
>>> 1) What are the units on the x-axis in 'Power Spectra 3' window - Hz?
>>> MHz?
>>> 2) How would one go about removing a specific band of frequencies? Is
>>> there a fslmaths command to remove a particular frequency in the middle?
>>>
>>> Thanks for your help, and happy new year!
>>>
>>> Annelene
>>>
>>>
>>>
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