[Mne_analysis] make_watershed_bem() does not make a BEM usable by setup_volume_source_space()
Alexandre Gramfort
alexandre.gramfort at inria.fr
Sat Oct 12 08:25:56 EDT 2019
External Email - Use Caution
hi,
mne-features has never been pushed to pypi. You should do:
pip install git+
https://github.com/mne-tools/mne-features.git#egg=mne_features
to install from the master branch.
Readme of mne-features needs to be updated or package should be released and
pushed to pypi.
Alex
On Thu, Oct 10, 2019 at 8:21 AM Bhuvaneshwari M <bhvnshwari at gmail.com>
> wrote:
>
>> 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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