[Neuroimaging] GC analysis with nitime

[Mike V]

Hi Ariel,

Thank you very much for your reply! I'll eagerly wait for the next release
:)

Best regards,
Mike

On Wed, 10 Jul 2019 at 04:26, Ariel Rokem <arokem at gmail.com> wrote:

> Hi Mike,
>
> Thanks for your email. Answers inline below:
>
> On Tue, Jul 9, 2019 at 3:12 PM Mike V <mikeltv95 at gmail.com> wrote:
>
>> Thank you Bennet, I'll wait for the next release then.
>> Best regards,
>> Mike
>>
>> On Sat, 6 Jul 2019 at 14:18, Bennet Fauber <bennet at umich.edu> wrote:
>>
>>> Mike,
>>>
>>> I reported the blank plots in an Issue at GitHub.  I think there may
>>> be more that is needed before they make a new release and refresh the
>>> tutorial page.
>>>
>>>     https://github.com/nipy/nitime/pull/176
>>>     https://github.com/nipy/nitime/issues/173
>>>
>>> Sorry, can't help with the rest.
>>>
>>> On Fri, Jul 5, 2019 at 7:37 PM Mike V <mikeltv95 at gmail.com> wrote:
>>> >
>>> > Hello,
>>> >
>>> > I'm following the Granger Causality tutorial in the nitime's webpage
>>> but I have few questions:
>>> >
>>> > 1- In the tutorial the values f_ub = 0.15 and f_lb = 0.02 are used for
>>> the bounds on the frequency band of interest. Are these values recommended
>>> for all resting state data-sets or do they depend on the particular
>>> acquisition parameters?
>>>
>>
> These are pretty reasonable for most fMRI data, with anything above 0.15
> Hz probably unrelated to the hemodynamic response and slow oscillations
> below 0.02 probably due to signal drift (but we also have a paper coming
> out soon that there are some interesting things going out in that infraslow
> range). But it really depends on your data and on your questions.
>
>
>> >
>>> > 2- I do not understand the causality plots (fig03 and fig04), they are
>>> both blank. What does it mean? I was expecting some variation like in the
>>> coherence and correlation matrices...
>>> >
>>>
>>
> Yes. As Bennet pointed out, this is a bug in the recent release. I really
> hope that we can fix that soon, but after a quick look, I am not quite sure
> what's going on, and have only limited time to devote to this in the next
> few weeks.
>
>
>> > 3- the tutorial shows the analysis of one single subject. How can I
>>> compute group statistics? Can I simply extract the values stored in g1 and
>>> then run a one sample t-test across all subjects' g1 scores?
>>> >
>>>
>>
> That seems like a reasonable approach.
>
>
>> > 4- how can I get GrangerAnalyzer to display significance?
>>> >
>>>
>>
> It's not designed to do so.
>
>
>> > 5- I noticed that the tutorial data has been motion corrected only. Is
>>> it not necessary to correct for other sources of noise like physiological
>>> noise and linear drift before computing GC?
>>> >
>>>
>>
> The filtering should help with that (see above).
>
> Hope that helps -- sorry about the slowness to respond and fix things,
>
> Ariel
>
>
>> > Many thanks in advance!
>>> >
>>> > Best regards,
>>> > Mike
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