[Mne_analysis] How to set atlas

Diptyajit Das bmedasdiptyajit at gmail.com
Wed Jan 23 11:09:36 EST 2019
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.in_label(label) takes a single argument i.e., single label. Just combine
the both labels and continue. For details, see this:
https://martinos.org/mne/stable/generated/mne.SourceEstimate.html?highlight=in_label#mne.SourceEstimate.in_label

On Wed, Jan 23, 2019 at 4:59 PM Vivek Sharma <vivek.sharma1510 at gmail.com>
wrote:

>         External Email - Use Caution
>
> When I run this command, label = mne.read_labels_from_annot(subject,
> hemi=hemi, parc='aparc', subjects_dir=subjects_dir, regexp=regexp)[0], with
> [0] at the end I could run the next command stc = stc.in_label(label),
> successfully but it reduces the number of vertices to 35, whereas when I do
> not use '[0]' at the end of command, I could not run the next command, it
> gives the following error:
> >>> label = mne.read_labels_from_annot('sub-CC721377_T1w', hemi='both',
> parc='aparc', subjects_dir=subjects_dir, regexp=None)
> Reading labels from parcellation...
>    read 34 labels from
> /home/vivek/Downloads/freesurfer/subjects/sub-CC721377_T1w/label/lh.aparc.annot
>    read 34 labels from
> /home/vivek/Downloads/freesurfer/subjects/sub-CC721377_T1w/label/rh.aparc.annot
> >>> stc_label.in_label(label)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/home/vivek/anaconda3/lib/python3.7/site-packages/mne/source_estimate.py",
> line 1197, in in_label
>     if label.subject is not None and self.subject is not None \
> AttributeError: 'list' object has no attribute 'subject'
>
>
> On Wed, Jan 23, 2019 at 6:52 PM Diptyajit Das <bmedasdiptyajit at gmail.com>
> wrote:
>
>>         External Email - Use Caution
>>
>> 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
>>>>> _______________________________________________
>>>>> Mne_analysis mailing list
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>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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>>>
>>>
>>> --
>>> Vivek Sharma
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
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>
>
>
> --
> Vivek Sharma
> _______________________________________________
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