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<body link="#0563C1" vlink="#954F72"><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 class="WordSection1">
<p class="MsoNormal"><span lang="EN-GB">Hi friends,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I have built a wrapper with mne to read and analyze data from the new Medtronic Percept implantable sensing enabled DBS device. The code is published here:
<a href="http://www.github.com/neuromodulation/icn_perceive">www.github.com/neuromodulation/icn_perceive</a>
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Unfortunately, handling correct dates is crucial for conversion into BIDS format. Everything was working fine in January. Now I have installed the code on a new machine and it creates the following issue:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">raw = ephys.mne_import_raw(raw_data.values.transpose() / 100000, list(raw_data.keys()), sfreq=sfreq,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif"> ...: ch_types='seeg', meas_date=(meas_date.timestamp(), 0))<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">raw.info['meas_date']<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">Out[38]: (1580223097.0, 0)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">raw.plot()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\IPython\core\interactiveshell.py", line 3331, in run_code<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> exec(code_obj, self.user_global_ns, self.user_ns)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "<ipython-input-39-f60196099aa7>", line 1, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> raw.plot()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\base.py", line 1378, in plot<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> show_scalebars=show_scalebars, verbose=verbose)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "<decorator-gen-138>", line 21, in plot_raw<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\viz\raw.py", line 336, in plot_raw<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> inds += [pick_types(info, meg=t, ref_meg=False, exclude=[])]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\pick.py", line 383, in pick_types<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> exclude = _check_info_exclude(info, exclude)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\pick.py", line 295, in _check_info_exclude<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> info._check_consistency()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\meas_info.py", line 693, in _check_consistency<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> % (prepend_error, repr(self['meas_date']),))<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red">RuntimeError: info["meas_date"] must be a datetime object in UTC or None, got "'(1580223097.0, 0)'"<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">raw.info['meas_date']=None<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">raw.plot()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">Out[41]: <Figure size 1600x825 with 4 Axes><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Now if I try to use the datetime object, the following error occurs:
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">raw = ephys.mne_import_raw(raw_data.values.transpose() / 100000, list(raw_data.keys()), sfreq=sfreq,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif"> ...: ch_types='seeg', meas_date=meas_date)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red">C:\Program Files\JetBrains\PyCharm Community Edition 2019.3\plugins\python-ce\helpers\pydev\_pydevd_bundle\pydevd_thrift.py:321: RuntimeWarning: Could not
get size for self.info<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> value = format % v<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif">raw.plot()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\IPython\core\interactiveshell.py", line 3331, in run_code<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> exec(code_obj, self.user_global_ns, self.user_ns)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "<ipython-input-49-f60196099aa7>", line 1, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> raw.plot()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\base.py", line 1378, in plot<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> show_scalebars=show_scalebars, verbose=verbose)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "<decorator-gen-138>", line 21, in plot_raw<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\viz\raw.py", line 336, in plot_raw<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> inds += [pick_types(info, meg=t, ref_meg=False, exclude=[])]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\pick.py", line 383, in pick_types<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> exclude = _check_info_exclude(info, exclude)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\pick.py", line 295, in _check_info_exclude<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> info._check_consistency()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> File "C:\code\Miniconda3\envs\icn\lib\site-packages\mne\io\meas_info.py", line 693, in _check_consistency<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> % (prepend_error, repr(self['meas_date']),))<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red">RuntimeError: info["meas_date"] must be a datetime object in UTC or None, got "'datetime.datetime(2020, 1, 28, 15, 51, 37)'"<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red">C:\Program Files\JetBrains\PyCharm Community Edition 2019.3\plugins\python-ce\helpers\pydev\_pydevd_bundle\pydevd_thrift.py:321: RuntimeWarning: Could not
get size for self.info<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"> value = format % v<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:red"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Any help is very much appreciated!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Best Julian from Berlin</span><span style="font-family:"Arial",sans-serif;mso-fareast-language:#1000"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">____________<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">Prof. Dr. med. Wolf-Julian Neumann<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">Assistant Professor - Interventional and Cognitive Neuromodulation<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">Movement Disorder and Neuromodulation Unit<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">Department of Neurology & Neuroradiology<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">Charité – Universitätsmedizin Berlin<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">T: +49 30 450 660 359<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB">M: +49 152 539 262 90<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:#1000"><a href="https://orcid.org/0000-0002-6758-9708"><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:#0563C1;mso-fareast-language:EN-GB">https://orcid.org/0000-0002-6758-9708</span></a></span><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:#1000"><a href="https://osf.io/uyg8w/"><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;color:#0563C1;mso-fareast-language:EN-GB">https://osf.io/uyg8w/</span></a></span><span lang="DE" style="font-size:8.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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