[Mne_analysis] Threshold connectivity matrix

Vivek Sharma vivek.sharma1510 at gmail.com
Fri Mar 1 03:23:32 EST 2019
Search archives:

        External Email - Use Caution        

Thanks Josh,
I tried changing the n_lines parameter in the plot_connectivity_circle()
function, it reduces the connections only. It still shows weak connections
or connections below desired value. I'll try other way you mentioned.

On Thu, Feb 28, 2019 at 11:57 PM Bear, Joshua <JOSHUA.BEAR at ucdenver.edu>
wrote:

> Hi Vivek,
>
> In those examples, I believe the thresholding occurs from the n_lines
> parameter in the plot_connectivity_circle() function. n_lines=300 means
> that only the 300 strongest connections are plotted. See the documentation
> for plot_connectivity_circle:
> https://martinos.org/mne/stable/generated/mne.viz.plot_connectivity_circle.html#mne.viz.plot_connectivity_circle
>
> If you wanted finer control over the threshold, you would need to either
> manipulate the values of the CON output (array) directly, or calculate an
> n_lines threshold that would capture your desired range. For example, if
> you wanted only those connections with a value > 0.3, you could count the
> number of connections with value > 0.3 and then use that number for your
> n_lines value. (I think this would work properly but have not tried it
> myself, so there might be some nuances to troubleshoot.)
>
> It wasn’t clear to me whether you meant significant connections or just an
> absolute value. The above suggestions threshold based on absolute value.
> You could use some statistical test appropriate for your own data to
> determine the absolute value, but depending on your goal and data there
> might be more direct methods.
>
> Cheers,
> Josh
>
>
> Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy
> University of Colorado and Children’s Hospital Colorado
> 13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138
> | Fax: 720-777-7285
>
>
>
> On Feb 28, 2019, at 2:18 AM, Vivek Sharma <vivek.sharma1510 at gmail.com>
> wrote:
>
>         External Email - Use Caution
>
> By significant connections I also mean the strongest connections. How to
> keep a threshold to remove weak connections.
>
> On Wed, Feb 27, 2019 at 11:08 AM Vivek Sharma <vivek.sharma1510 at gmail.com>
> wrote:
>
>> Dear Marijn,
>> Its a single subject MEG data.
>> By significant I mean, if you look at the figure in the following example:
>>
>> https://martinos.org/mne/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py
>> on lower right, it shows a bar that display the strength of those
>> connections with values 0.4-0.6. When I plot for my data the bar displays
>> values from 0.15-0.20 and shows the connections below 0.15 also. How can I
>> restrict it to show only connections above 0.15?
>>
>> On Tue, Feb 26, 2019 at 6:17 PM Marijn van Vliet <w.m.vanvliet at gmail.com>
>> wrote:
>>
>>>         External Email - Use Caution
>>>
>>> Dear Vivek,
>>>
>>> significant in what way? If you have multiple subjects, you can compute
>>> a t-statistic for each connection. If you have multiple experimental
>>> conditions, you can do a paired t-test between conditions…. Could you tell
>>> us a bit more about the data?
>>>
>>> best,
>>> Marijn.
>>>
>>> > On 26 Feb 2019, at 10:01, Vivek Sharma <vivek.sharma1510 at gmail.com>
>>> wrote:
>>> >
>>> >         External Email - Use Caution
>>> >
>>> >
>>> > I'm using the following example code to compute connectivity.
>>> >
>>> https://martinos.org/mne/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py
>>> >
>>> > How can I apply statistical threshold to have only significant
>>> connections?
>>> >
>>> > --
>>> > Vivek Sharma
>>> > _______________________________________________
>>> > Mne_analysis mailing list
>>> > Mne_analysis at nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>>
>> --
>> Vivek Sharma
>>
>
>
> --
> Vivek Sharma
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>         External Email - Use Caution
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis



-- 
Vivek Sharma
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190301/5949eabd/attachment-0001.html 


More information about the Mne_analysis mailing list