<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div dir="ltr">hi,<br><br>mne-features has never been pushed to pypi. You should do:<br><br>pip install git+<a href="https://github.com/mne-tools/mne-features.git#egg=mne_features" target="_blank">https://github.com/mne-tools/mne-features.git#egg=mne_features</a><br><br>to install from the master branch.<div><br></div><div>Readme of mne-features needs to be updated or package should be released and</div><div>pushed to pypi.<br><div><br></div><div>Alex</div></div></div><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">On Thu, Oct 10, 2019 at 8:21 AM Bhuvaneshwari M <<a href="mailto:bhvnshwari@gmail.com" target="_blank">bhvnshwari@gmail.com</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr">Hi,<div> Seasons' greetings.</div><div> 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:</div><div><br></div><div>(base) C:\Users\Admin>pip install mne-features<br>Collecting mne-features<br> Could not find a version that satisfies the requirement mne-features (from versions: )<br>No matching distribution found for mne-features</div><div><br></div><div>the following Requirement are also satisfied:</div><div><p style="box-sizing:border-box;margin-top:0px;margin-bottom:16px;color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji";font-size:16px">These are the dependencies to use MNE-Features:</p><ul style="box-sizing:border-box;padding-left:2em;margin-top:0px;margin-bottom:16px;color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji";font-size:16px"><li style="box-sizing:border-box">numpy (>=1.8)</li><li style="box-sizing:border-box;margin-top:0.25em">matplotlib (>=1.3)</li><li style="box-sizing:border-box;margin-top:0.25em">scipy (>=0.19)</li><li style="box-sizing:border-box;margin-top:0.25em">numba (>=0.37)</li><li style="box-sizing:border-box;margin-top:0.25em">scikit-learn (>=0.19)</li><li style="box-sizing:border-box;margin-top:0.25em">mne (>=0.14)</li><li style="box-sizing:border-box;margin-top:0.25em">PyWavelets (>=0.5.2)</li><li style="box-sizing:border-box;margin-top:0.25em">pandas (>=0.20)</li></ul><div><font color="#24292e" face="-apple-system, BlinkMacSystemFont, Segoe UI, Helvetica, Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji"><span style="font-size:16px">please help me out.</span></font></div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><font face="'times new roman', serif" color="#999900">regards,<br></font><div><b><i><font face="'times new roman', serif" color="#999900">M.Bhuvaneshwari,<br></font></i></b></div><div><b style="color:rgb(153,153,0);font-family:"times new roman",serif"><i>Research Scholar,</i></b><br></div></div><div><b style="color:rgb(153,153,0);font-family:"times new roman",serif"><i>Karunya Institute of technology and Sciences</i></b></div><div><font color="#999900" face="times new roman, serif"><b><i>Coimbatore.<br></i></b></font></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Oct 5, 2019 at 12:51 AM Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr">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.<div><br></div><div>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.<div><br></div><div>Eric</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Oct 4, 2019 at 7:21 PM Christian O'Reilly <<a href="mailto:christian.oreilly@gmail.com" target="_blank">christian.oreilly@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div>Hi, <br></div><div><br></div><div><div>At line 1182 of <a href="https://github.com/mne-tools/mne-python/blob/maint/0.19/mne/bem.py" target="_blank">https://github.com/mne-tools/mne-python/blob/maint/0.19/mne/bem.py</a> 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 <a href="https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py" target="_blank">https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py</a>) and then crash because this surface id is not found in the BEM (stack trace below).</div><div><br></div><div>I used <br></div><div><br></div><div>mne.bem.make_watershed_bem(fs_subject, subjects_dir=subjects_dir, <br> overwrite=False, show=True)</div><div><br></div><div>to make the BEM and <br></div><div><br></div><div>vol_src = setup_volume_source_space(<br> subject, mri=fname_aseg, pos=10.0, bem=fname_model,<br> add_interpolator=False, volume_label=labels_vol, subjects_dir=subjects_dir)</div><div><br></div><div>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?</div><div><br></div><div>Best,</div><div><br></div><div>Christian<br></div><br>---------------------------------------------------------------------------<br>ValueError Traceback (most recent call last)<br><ipython-input-27-be76d29cf63d> in <module><br> 4 vol_src = setup_volume_source_space(pos=10.0, bem=fname_model,<br> 5 add_interpolator=False, # just for speed, usually use True<br>----> 6 mri=fname_aseg)<br> 7 # Generate the mixed source space<br> 8 src += vol_src<br><br></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)<br><br>~/mne-python/mne/utils/_logging.py in wrapper(*args, **kwargs)<br> 88 with use_log_level(verbose_level):<br> 89 return function(*args, **kwargs)<br>---> 90 return function(*args, **kwargs)<br> 91 return FunctionMaker.create(<br> 92 function, 'return decfunc(%(signature)s)',<br><br>~/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)<br> 1704 # read bem surface in the MRI coordinate frame<br> 1705 surf = read_bem_surfaces(bem, s_id=FIFF.FIFFV_BEM_SURF_ID_BRAIN,<br>-> 1706 verbose=False)<br> 1707 <a href="http://logger.info" target="_blank">logger.info</a>('Loaded inner skull from %s (%d nodes)'<br> 1708 % (bem, surf['np']))<br><br></home/oreillyc/mne-python/mne/externals/decorator.py:decorator-gen-50> in read_bem_surfaces(fname, patch_stats, s_id, verbose)<br><br>~/mne-python/mne/utils/_logging.py in wrapper(*args, **kwargs)<br> 87 # set it back if we get an exception<br> 88 with use_log_level(verbose_level):<br>---> 89 return function(*args, **kwargs)<br> 90 return function(*args, **kwargs)<br> 91 return FunctionMaker.create(<br><br>~/mne-python/mne/bem.py in read_bem_surfaces(fname, patch_stats, s_id, verbose)<br> 1270 surf = [s for s in surf if s is not None]<br> 1271 if not len(surf) == 1:<br>-> 1272 raise ValueError('surface with id %d not found' % s_id)<br> 1273 else:<br> 1274 surf = list()<br><br>ValueError: surface with id 1 not found</div></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
</blockquote></div></div>