[Mne_analysis] make_watershed_bem() does not make a BEM usable by setup_volume_source_space()

[Bhuvaneshwari M]

        External Email - Use Caution        

Hi,
   Seasons' greetings.
           I am new to MNE and also to python. How to install mne-features
in anaconda navigator. I tried with pip install mne-features, but shows the
following error:

(base) C:\Users\Admin>pip install mne-features
Collecting mne-features
  Could not find a version that satisfies the requirement mne-features
(from versions: )
No matching distribution found for mne-features

the following Requirement are also satisfied:

These are the dependencies to use MNE-Features:

   - numpy (>=1.8)
   - matplotlib (>=1.3)
   - scipy (>=0.19)
   - numba (>=0.37)
   - scikit-learn (>=0.19)
   - mne (>=0.14)
   - PyWavelets (>=0.5.2)
   - pandas (>=0.20)

please help me out.
regards,

*M.Bhuvaneshwari,*
*Research Scholar,*
*Karunya Institute of technology and Sciences*

*Coimbatore.*


On Sat, Oct 5, 2019 at 12:51 AM Eric Larson <larson.eric.d at gmail.com> wrote:

>         External Email - Use Caution
>
> That function just makes the surfaces, plus the subject's head FIF. I
> suspect you've tried to use `subject-head.fif` as your BEM, which will not
> work.
>
> You need to use `mne.make_bem_model` and `mne.make_bem_solution` to
> actually make the BEM itself from the surfaces `make_watershed_bem`
> produced, choosing along the way if you want a 1-layer or 3-layer model.
> You can then save these to disk and load them when you need them.
>
> Eric
>
>
> On Fri, Oct 4, 2019 at 7:21 PM Christian O'Reilly <
> christian.oreilly at gmail.com> wrote:
>
>>         External Email - Use Caution
>>
>> Hi,
>>
>> At line 1182 of
>> https://github.com/mne-tools/mne-python/blob/maint/0.19/mne/bem.py
>> mne.bem.make_watershed_bem() is creating the BEM FIF file using
>> FIFF.FIFFV_BEM_SURF_ID_HEAD (==4). When using this BEM file for source
>> modeling mne.setup_volume_source_space() expect
>> FIFF.FIFFV_BEM_SURF_ID_BRAIN (==1) (line 1705
>> https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py)
>> and then crash because this surface id is not found in the BEM (stack trace
>> below).
>>
>> I used
>>
>> mne.bem.make_watershed_bem(fs_subject, subjects_dir=subjects_dir,
>>                            overwrite=False, show=True)
>>
>> to make the BEM and
>>
>> vol_src = setup_volume_source_space(
>>     subject, mri=fname_aseg, pos=10.0, bem=fname_model,
>>     add_interpolator=False, volume_label=labels_vol,
>> subjects_dir=subjects_dir)
>>
>> to build the source space. Do you think it is a bug (I'll make a ticker
>> if so), or does it look like I used these functions not correctly?
>>
>> Best,
>>
>> Christian
>>
>>
>> ---------------------------------------------------------------------------
>> ValueError                                Traceback (most recent call
>> last)
>> <ipython-input-27-be76d29cf63d> in <module>
>>       4 vol_src = setup_volume_source_space(pos=10.0, bem=fname_model,
>>       5     add_interpolator=False,  # just for speed, usually use True
>> ----> 6     mri=fname_aseg)
>>       7 # Generate the mixed source space
>>       8 src += vol_src
>>
>> </home/oreillyc/mne-python/mne/externals/decorator.py:decorator-gen-90>
>> in setup_volume_source_space(subject, pos, mri, sphere, bem, surface,
>> mindist, exclude, subjects_dir, volume_label, add_interpolator, verbose)
>>
>> ~/mne-python/mne/utils/_logging.py in wrapper(*args, **kwargs)
>>      88             with use_log_level(verbose_level):
>>      89                 return function(*args, **kwargs)
>> ---> 90         return function(*args, **kwargs)
>>      91     return FunctionMaker.create(
>>      92         function, 'return decfunc(%(signature)s)',
>>
>> ~/mne-python/mne/source_space.py in setup_volume_source_space(subject,
>> pos, mri, sphere, bem, surface, mindist, exclude, subjects_dir,
>> volume_label, add_interpolator, verbose)
>>    1704             # read bem surface in the MRI coordinate frame
>>    1705             surf = read_bem_surfaces(bem,
>> s_id=FIFF.FIFFV_BEM_SURF_ID_BRAIN,
>> -> 1706                                      verbose=False)
>>    1707             logger.info('Loaded inner skull from %s (%d nodes)'
>>    1708                         % (bem, surf['np']))
>>
>> </home/oreillyc/mne-python/mne/externals/decorator.py:decorator-gen-50>
>> in read_bem_surfaces(fname, patch_stats, s_id, verbose)
>>
>> ~/mne-python/mne/utils/_logging.py in wrapper(*args, **kwargs)
>>      87             # set it back if we get an exception
>>      88             with use_log_level(verbose_level):
>> ---> 89                 return function(*args, **kwargs)
>>      90         return function(*args, **kwargs)
>>      91     return FunctionMaker.create(
>>
>> ~/mne-python/mne/bem.py in read_bem_surfaces(fname, patch_stats, s_id,
>> verbose)
>>    1270             surf = [s for s in surf if s is not None]
>>    1271             if not len(surf) == 1:
>> -> 1272                 raise ValueError('surface with id %d not found' %
>> s_id)
>>    1273         else:
>>    1274             surf = list()
>>
>> ValueError: surface with id 1 not found
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