Hi there:
I use AFNI 3D despike. But, I run a mixture of FSL and SPM12 for my rest pipeline. If you are running a pure FSL pipeline I think there is also a despiking utility in FSL -- the FSL experts will probably be able to weigh in here :)
Good luck!
Nina
On Sun, 8 Jan 2017, Eelco Van Duinkerken wrote:
> Hi Nina,
>
> Thank you very much for your quick reply.
>
> We are also not a fan of scrubbing, but he letĒs give it a try, sometimes reviewers can be very persistent.
>
> I have not considered despiking yet, but will give it a try as well. Do you have any software of preference you think works well?
>
> Thanks,
>
> Eelco
>
>
>> On 8 Jan 2017, at 16:39, Nina de Lacy <[log in to unmask]> wrote:
>>
>> Hi Eelco:
>>
>> I'm not personally a fan of scrubbing, and there are arguments to be made against it you can cite from the literature -- though I would of course support checking something out so you could respond to your reviewer with a sub-analysis presented in the response letter (and/or paper) to demonstrate that scrubbing didn't change your results of interest.
>>
>> My main purpose in writing is to offer the thought that if you haven't already done it, an alternative approach which does not involve removing timepoints from your data is despiking, which essentially employs interpolation. Many packages offer despiking capability.
>>
>> Best
>> Nina
>>
>>
>> On Sun, 8 Jan 2017, Eelco Van Duinkerken wrote:
>>
>>> Dear all,
>>>
>>> Using my resting-state fMRI scans I have calculated eigenvector centrality in my study with the standard FSL preprocessing (i.e. mcflirt, slice timing correction, smoothing and hp filtering).
>>>
>>> One of the reviewers of the paper now asks to scrub the data and then repeat the analysis. I know there can be said a lot against scrubbing, but I wanted to give it a try and actually see what happens with the data.
>>>
>>> IĒve used fsl_motion_outliers on my raw and unpreprocessed fMRI data using dvars as output. On the fsl wiki it says this can then be added to FEAT, but unfortunately, I am only using FEAT for the preprocessing.
>>>
>>> Is there any part of FSL, or could be any other package, that is able to scrub the data based on the output of fsl_motion_outliers? I couldnĒt find anything about this in the list. There is always the option to remove volumes by hand, but given the sample size that would be pretty time consuming and so that is my last resort.
>>>
>>> Thanks!
>>>
>>> Eelco
>>>
>>
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