<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"><div>.in_label(label) takes a single argument i.e., single label. Just combine the both labels and continue. For details, see this:</div><div><a href="https://martinos.org/mne/stable/generated/mne.SourceEstimate.html?highlight=in_label#mne.SourceEstimate.in_label">https://martinos.org/mne/stable/generated/mne.SourceEstimate.html?highlight=in_label#mne.SourceEstimate.in_label</a><br> </div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 23, 2019 at 4:59 PM Vivek Sharma <<a href="mailto:vivek.sharma1510@gmail.com">vivek.sharma1510@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 dir="ltr"><div dir="ltr">When I run this command, label = mne.read_labels_from_annot(subject, hemi=hemi, parc='aparc', subjects_dir=subjects_dir, regexp=regexp)[0], with [0] at the end I could run the next command stc = stc.in_label(label), successfully but it reduces the number of vertices to 35, whereas when I do not use '[0]' at the end of command, I could not run the next command, it gives the following error:<div><div><div>>>> label = mne.read_labels_from_annot('sub-CC721377_T1w', hemi='both', parc='aparc', subjects_dir=subjects_dir, regexp=None)</div><div>Reading labels from parcellation...</div><div> read 34 labels from /home/vivek/Downloads/freesurfer/subjects/sub-CC721377_T1w/label/lh.aparc.annot</div><div> read 34 labels from /home/vivek/Downloads/freesurfer/subjects/sub-CC721377_T1w/label/rh.aparc.annot</div></div><div>>>> stc_label.in_label(label)</div><div>Traceback (most recent call last):</div><div> File "<stdin>", line 1, in <module></div><div> File "/home/vivek/anaconda3/lib/python3.7/site-packages/mne/source_estimate.py", line 1197, in in_label</div><div> if label.subject is not None and self.subject is not None \</div><div>AttributeError: 'list' object has no attribute 'subject'</div></div><div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail-m_3467589676815621040gmail_attr">On Wed, Jan 23, 2019 at 6:52 PM Diptyajit Das <<a href="mailto:bmedasdiptyajit@gmail.com" target="_blank">bmedasdiptyajit@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 dir="ltr"><div>Follow this:</div><div><a href="https://github.com/mne-tools/mne-python/issues/5850" target="_blank">https://github.com/mne-tools/mne-python/issues/5850</a></div><div><br></div><div>best,<br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail-m_3467589676815621040gmail-m_8851470572228470334gmail_attr">On Tue, Jan 22, 2019 at 11:18 AM Vivek Sharma <<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@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">Hi,<div>Thanks for the code.</div><div>I tried with this method but it reduces the number of vertices to 35, I want it to be 68 according to Desikan atlas.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail-m_3467589676815621040gmail-m_8851470572228470334gmail-m_-4390130815623545218gmail_attr">On Thu, Jan 17, 2019 at 5:12 PM Diptyajit Das <<a href="mailto:bmedasdiptyajit@gmail.com" target="_blank">bmedasdiptyajit@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 dir="ltr"><div>Hi, <br></div><div><br></div><div>You do cortical parcellation by using some atlas. I think what you meant is to restrict the dipoles activity to some particular brain regions. For that, you need to pass the 'label' during source estimation or you can do something like this after the source estimate:</div><div><br></div><div>code:<br></div><div>regexp = 'bankssts' # name the brain region that you are interested in</div><div>hemi = 'both' # taking both hemisphere<br></div><div><span></span>label =
mne.read_labels_from_annot(subject, hemi=hemi, parc='aparc',
subjects_dir=subjects_dir, regexp=regexp)[0] # read the label of the particular region based on Desikan atlas (i.e., defined by 'aparc')</div><div>stc =
stc.in_label(label) # restrict the dipoles to that particular label<br><p style="margin-bottom:0in;line-height:100%"><br></p><p style="margin-bottom:0in;line-height:100%">best,</p><p style="margin-bottom:0in;line-height:100%">Dip</p></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail-m_3467589676815621040gmail-m_8851470572228470334gmail-m_-4390130815623545218gmail-m_-609284873714973337gmail_attr">On Thu, Jan 17, 2019 at 12:05 PM Vivek Sharma <<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@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 dir="ltr">Okay.<div>The source estimate file I'm getting consists of 8175 vertices (SourceEstimate | 8175 vertices) , I wanted to reduce the number of vertices to the ROIs, in my case I wanted to use Desikan atlas.</div><div>How can I reduce the number of vertices, specific to certain atlases?</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail-m_3467589676815621040gmail-m_8851470572228470334gmail-m_-4390130815623545218gmail-m_-609284873714973337gmail-m_5803563496366269002gmail_attr">On Thu, Jan 17, 2019 at 2:10 PM Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</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"> External Email - Use Caution <br>
<br>
make_watershed_bem uses an atlas to get a good skull segmentation<br>
<br>
it's not an atlas of the cortical surface as you suggest<br>
<br>
HTH<br>
A<br>
<br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail-m_3467589676815621040gmail-m_8851470572228470334gmail-m_-4390130815623545218gmail-m_-609284873714973337gmail-m_5803563496366269002gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="font-size:12.8px">Vivek Sharma</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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