<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>Hello everyone,</div><div><br></div>I am almost new to MNE, Please be patient with me.<div>I am trying to calculate the functional network from raw resting state MEG data from <a href="http://How_to_Build_a_Functional_Connectomic_Biomarker_for_Mild_Cognitive_Impairment_from_Source_Reconstructed_MEG_Resting-State_Activity_-_Raw_data_I_Controls_/6210158">here</a>.</div><div>I am following this example: <br></div><div><div><a href="https://mne.tools/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html">Compute source space connectivity and visualize it using a circular graph</a></div><div><br></div><div>The problem is there is no <b>meg-inv.fif</b> file in the dataset.</div><div>an I am stuck in these lines:</div><div><br></div><div><pre style="box-sizing:border-box;overflow:auto;font-family:"Source Code Pro",monospace;font-size:15px;padding:10px;margin-top:0px;margin-bottom:10.5px;line-height:1.42857;word-break:break-all;color:rgb(44,62,80);background-color:rgb(250,250,250);border:1px solid rgb(204,204,204);border-radius:4px"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit"><pre style="box-sizing:border-box;overflow:auto;font-family:"Source Code Pro",monospace;padding:10px;margin-top:0px;margin-bottom:10.5px;line-height:1.42857;word-break:break-all;border:1px solid rgb(204,204,204);border-radius:4px"><a href="https://mne.tools/stable/generated/mne.minimum_norm.InverseOperator.html#mne.minimum_norm.InverseOperator" title="mne.minimum_norm.InverseOperator" class="gmail-sphx-glr-backref-module-mne-minimum_norm gmail-sphx-glr-backref-type-py-class gmail-sphx-glr-backref-instance" style="box-sizing:border-box;text-decoration-line:none;font-weight:600;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">inverse_operator</span></a> <span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102);font-weight:inherit;font-style:inherit">=</span> <a href="https://mne.tools/stable/generated/mne.minimum_norm.read_inverse_operator.html#mne.minimum_norm.read_inverse_operator" title="mne.minimum_norm.read_inverse_operator" class="gmail-sphx-glr-backref-module-mne-minimum_norm gmail-sphx-glr-backref-type-py-function" style="box-sizing:border-box;text-decoration-line:none;font-weight:600;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">read_inverse_operator</span></a><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">(</span><a href="https://docs.python.org/3/library/stdtypes.html#str" title="builtins.str" class="gmail-sphx-glr-backref-module-builtins gmail-sphx-glr-backref-type-py-class gmail-sphx-glr-backref-instance" style="box-sizing:border-box;text-decoration-line:none;font-weight:inherit;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">fname_inv</span></a><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">)</span></pre></span></pre><pre style="box-sizing:border-box;overflow:auto;font-family:"Source Code Pro",monospace;font-size:15px;padding:10px;margin-top:0px;margin-bottom:10.5px;line-height:1.42857;word-break:break-all;color:rgb(44,62,80);background-color:rgb(250,250,250);border:1px solid rgb(204,204,204);border-radius:4px"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">stcs</span> <span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102);font-weight:inherit;font-style:inherit">=</span> <a href="https://mne.tools/stable/generated/mne.minimum_norm.apply_inverse_epochs.html#mne.minimum_norm.apply_inverse_epochs" title="mne.minimum_norm.apply_inverse_epochs" class="gmail-sphx-glr-backref-module-mne-minimum_norm gmail-sphx-glr-backref-type-py-function" style="box-sizing:border-box;text-decoration-line:none;font-weight:600;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">apply_inverse_epochs</span></a><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">(</span><a href="https://mne.tools/stable/generated/mne.Epochs.html#mne.Epochs" title="mne.Epochs" class="gmail-sphx-glr-backref-module-mne gmail-sphx-glr-backref-type-py-class gmail-sphx-glr-backref-instance" style="box-sizing:border-box;text-decoration-line:none;font-weight:600;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">epochs</span></a><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">,</span> <a href="https://mne.tools/stable/generated/mne.minimum_norm.InverseOperator.html#mne.minimum_norm.InverseOperator" title="mne.minimum_norm.InverseOperator" class="gmail-sphx-glr-backref-module-mne-minimum_norm gmail-sphx-glr-backref-type-py-class gmail-sphx-glr-backref-instance" style="box-sizing:border-box;text-decoration-line:none;font-weight:600;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">inverse_operator</span></a><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">,</span> <a href="https://docs.python.org/3/library/functions.html#float" title="builtins.float" class="gmail-sphx-glr-backref-module-builtins gmail-sphx-glr-backref-type-py-class gmail-sphx-glr-backref-instance" style="box-sizing:border-box;text-decoration-line:none;font-weight:inherit;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">lambda2</span></a><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">,</span> <a href="https://docs.python.org/3/library/stdtypes.html#str" title="builtins.str" class="gmail-sphx-glr-backref-module-builtins gmail-sphx-glr-backref-type-py-class gmail-sphx-glr-backref-instance" style="box-sizing:border-box;text-decoration-line:none;font-weight:inherit;font-style:inherit"><span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">method</span></a><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">,</span>
<span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">pick_ori</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102);font-weight:inherit;font-style:inherit">=</span><span class="gmail-s2" style="box-sizing:border-box;color:rgb(186,33,33);font-weight:inherit;font-style:inherit">"normal"</span><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">,</span> <span class="gmail-n" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">return_generator</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102);font-weight:inherit;font-style:inherit">=</span><span class="gmail-kc" style="box-sizing:border-box;color:rgb(0,128,0);font-weight:bold;font-style:inherit">True</span><span class="gmail-p" style="box-sizing:border-box;color:inherit;font-weight:inherit;font-style:inherit">)</span></pre></div><div><span style="font-size:13px;font-family:Arial,sans-serif;background-color:rgb(248,248,248)">Gramfort, 2013. MEG and EEG data analysis with MNE-Python. </span><i style="font-size:13px;font-family:Arial,sans-serif;background-color:rgb(248,248,248)">Frontiers in neuroscience</i><span style="font-size:13px;font-family:Arial,sans-serif;background-color:rgb(248,248,248)">, </span><i style="font-size:13px;font-family:Arial,sans-serif;background-color:rgb(248,248,248)">7</i><span style="font-size:13px;font-family:Arial,sans-serif;background-color:rgb(248,248,248)">, p.267.</span><br></div><div>This article clearly explain why we need a SourceEstimate object<span style="color:rgb(186,33,33);font-style:inherit;font-weight:inherit;background-color:rgb(250,250,250);font-family:"Source Code Pro",monospace;font-size:15px"></span></div><div><br></div><div>Is it still possible to calculate the functional network from this dataset or I should look for something else?</div><div><br></div><div>here is the output of <b><font color="#ff0000"><a href="http://raw.info">raw.info</a></font></b>:</div><div><b>MADCN0001_tsss_mc.fif</b></div><div><Info | 23 non-empty values<br> acq_pars: ACQch001 110113 ACQch002 110112 ACQch003 110111 ACQch004 110122 ...<br> bads: []<br> ch_names: MEG0113, MEG0112, MEG0111, MEG0122, MEG0123, MEG0121, MEG0132, ...<br> chs: 204 GRAD, 102 MAG, 1 EEG, 3 STIM, 9 CHPI<br> custom_ref_applied: False<br> description: Vectorview system<br> dev_head_t: MEG device -> head transform<br> dig: 322 items (3 Cardinal, 4 HPI, 315 Extra)<br> events: 1 item (list)<br> experimenter: Common account for MEG work (meg)<br> file_id: 4 items (dict)<br> highpass: 0.1 Hz<br> hpi_meas: 1 item (list)<br> hpi_results: 1 item (list)<br> hpi_subsystem: 2 items (dict)<br> line_freq: 50.0<br> lowpass: 330.0 Hz<br> meas_date: 2013-11-05 12:09:28 UTC<br> meas_id: 4 items (dict)<br> nchan: 319<br> proc_history: 1 item (list)<br> proj_id: 1 item (ndarray)<br> proj_name: qsm<br> projs: []<br> sfreq: 1000.0 Hz<br> subject_info: 7 items (dict)<br>><br></div><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><pre>Abolfazl Ziaeemehr
Department of Physics,
PhD student in Computational Physics
Institute for Advanced Studies in Basic Sciences (IASBS)<br>Tel: 0919 607 4296<br>Page: <a href="http://iasbs.ac.ir/~a.ziaeemehr" target="_blank">iasbs.ac.ir/~a.ziaeemehr</a><br><br></pre></div></div></div></div></div></div></div>