[Mne_analysis] How to set atlas

Diptyajit Das bmedasdiptyajit at gmail.com
Wed Jan 23 08:21:05 EST 2019
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Follow this:
https://github.com/mne-tools/mne-python/issues/5850

best,

On Tue, Jan 22, 2019 at 11:18 AM Vivek Sharma <vivek.sharma1510 at gmail.com>
wrote:

>         External Email - Use Caution
>
> Hi,
> Thanks for the code.
> I tried with this method but it reduces the number of vertices to 35, I
> want it to be 68 according to Desikan atlas.
>
> On Thu, Jan 17, 2019 at 5:12 PM Diptyajit Das <bmedasdiptyajit at gmail.com>
> wrote:
>
>>         External Email - Use Caution
>>
>> Hi,
>>
>> You do cortical parcellation by using some atlas. I think what you meant
>> is to restrict the dipoles activity to some particular brain regions. For
>> that,  you need to pass the 'label'  during source estimation or you can do
>> something like this after the source estimate:
>>
>> code:
>> regexp = 'bankssts'     # name the brain region that you are interested in
>> hemi = 'both'  # taking both hemisphere
>> label = mne.read_labels_from_annot(subject, hemi=hemi, parc='aparc',
>> subjects_dir=subjects_dir, regexp=regexp)[0]    # read the label of the
>> particular region based on Desikan atlas (i.e., defined by 'aparc')
>> stc = stc.in_label(label)  # restrict the dipoles to that particular label
>>
>>
>> best,
>>
>> Dip
>>
>> On Thu, Jan 17, 2019 at 12:05 PM Vivek Sharma <vivek.sharma1510 at gmail.com>
>> wrote:
>>
>>>         External Email - Use Caution
>>>
>>> Okay.
>>> The source estimate file I'm getting consists of 8175 vertices
>>> (SourceEstimate  |  8175 vertices) , I wanted to reduce the number of
>>> vertices to the ROIs, in my case I wanted to use Desikan atlas.
>>> How can I reduce the number of vertices, specific to certain atlases?
>>>
>>> On Thu, Jan 17, 2019 at 2:10 PM Alexandre Gramfort <
>>> alexandre.gramfort at inria.fr> wrote:
>>>
>>>>         External Email - Use Caution
>>>>
>>>> make_watershed_bem uses an atlas to get a good skull segmentation
>>>>
>>>> it's not an atlas of the cortical surface as you suggest
>>>>
>>>> HTH
>>>> A
>>>>
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>>>
>>>
>>> --
>>> Vivek Sharma
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>
>
> --
> Vivek Sharma
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