[Mne_analysis] How to set atlas

Dan McCloy dan.mccloy at gmail.com
Mon Feb 4 13:25:47 EST 2019
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This line:
*label = mne.read_labels_from_annot('subject', hemi='both', parc='aparc',
subjects_dir=subjects_dir, regexp=None)[0]*

selects the alphabetically first label from the parcellation*.* Is that
really what you want?  More clearly: mne.read_labels_from_annot returns a
list of labels **sorted by label name (ascending)**.  Perhaps you're
getting the wrong number of vertices because you're selecting the wrong
label?

On Mon, Feb 4, 2019 at 1:09 AM Vivek Sharma <vivek.sharma1510 at gmail.com>
wrote:

>         External Email - Use Caution
>
> I'm still not able to reduce the number of vertices to 68.
> let me again explain my problem with more detail:
> I'm using the following command to generate source estimates...
>
> *stc = mne.minimum_norm.apply_inverse_raw(raw, inverse_operator, lambda2,
> method='eLORETA', label=None, start=60, stop=240, nave=1, time_func=None,
> pick_ori=None, buffer_size=None, prepared=False, method_params=None,
> verbose=None)*
>
> The output of above command contains 8175 vertices and I want to reduce
> the number of vertices to 68 which is according to Desikan atlas.
> To reduce the vertices I use the following code:
>
>
> *label = mne.read_labels_from_annot('subject', hemi='both', parc='aparc',
> subjects_dir=subjects_dir, regexp=None)[0]*
> *stc1 = stc.in_label(label)*
>
>
> Now the stc1 contain 35 vertices but I want 68 (Desikan)
>
> On Wed, Jan 23, 2019 at 9:40 PM Diptyajit Das <bmedasdiptyajit at gmail.com>
> wrote:
>
>>         External Email - Use Caution
>>
>> .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
>>>>>>> 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
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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
>>> _______________________________________________
>>> 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
> _______________________________________________
> 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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