<div dir="ltr">Dear Jan-Mathijs,<div><br></div><div>Many thanks for your quick reply! </div><div><br></div><div>There is no 'coordsys' field in mri when I read it in with ft_read_mri. When I run ft_determine_coordsys, the output coordsys is 'ras'. However, the origin of the coordinate system of the MRI is not a landmark. As you can see in Figure 1 in the previous email that I sent, it appears to be shifted downward in the Z-axis relative to the anterior commissure. My reason for running ft_volumerealign was to re-center the origin of the MRI coordinate system at the anterior commissure.</div><div><br></div><div>However, if I just set mri.coordsys = 'ras', delete the ft_volumerealign step, and then run the rest of my pipeline unchanged, my visualization of the source activity changes slightly, but it is still very misaligned to the subject's MRI; please see below.</div><div><br></div><div>sourcemodel and headmodel are both in units of 'mm'. tlock.grad is in units of 'cm', but it appears that FieldTrip converts these 'cm' units to 'mm' units during ft_prepare_leadfield (according to the output in the command window).</div><div><br></div><div>'positions' is a 591x3 matrix consisting of the MNI coordinates of 591 voxels of interest. These generally fall into four regions of interest, which were defined in a previous study: fusiform face area, thalamus, left dorsolateral prefrontal cortex, and right dorsolateral prefrontal cortex. I have attached the positions as a .mat file below.</div><div><br></div><div>Please let me know if you would like any further information!</div><div><br></div><div>Best regards,</div><div>Kenneth</div><div><br></div><img src="cid:ii_m2jcyjlj0" alt="Screenshot 2024-10-21 at 22.36.37.png" width="562" height="425"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 21, 2024 at 10:04 PM Schoffelen, J.M. (Jan Mathijs) via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</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">
<div>
Hi Kenneth,
<div><br>
</div>
<div>Assuming that the ‘source_placebo’ variable you refer to in the second part of your message has been obtained in a similar way as the ‘source’ variable in the first part of your message, to me it looks that there’s something off with the ‘positions’ that
you start out with. Without additional information about those it is difficult to comment.</div>
<div><br>
</div>
<div>Besides this, I suggest that you go through your pipeline step-by-step and visualize in more detail the objects that go in and out of the individual function calls.</div>
<div>Specificallly you should pay attention to whether the coordinate systems and geometric units are aligned (FieldTrip might be forgiving with respect to units, but it never hurts to explicitly equalize them across data objects (volume conductor model, source
grid, sensor defintion). It goes without saying that FieldTrip is not forgiving with respect to differences in coordinate systems. Those should match across input objects. It’s not often that I have seen an MEG system with the sensors defined in ‘acpc’ coordinates,
so I doubt whether the first alignment step to obtain mri_realigned from the original mri image is correct.</div>
<div><br>
</div>
<div>Good luck</div>
<div>Jan-Mathijs</div>
<div><br id="m_-8041626596201145286lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On 21 Oct 2024, at 18:58, Kenneth Shinozuka via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Hello,
<div><br>
</div>
<div>I am currently source-localizing some MEG data in such a way that I am inverse-warping a template of MNI coordinates to each individual's anatomical MRI. I am running the following code:</div>
<div><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"></span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">mri = ft_read_mri(mri_filename);</span></div>
<div><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><br>
</span></div>
<div><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg = [];
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.method =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'interactive';
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.coordsys =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'acpc'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(0,128,19)">% the desired coordinate system</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">mri_realigned
= ft_volumerealign(cfg, mri); </span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg = [];
</span>cfg.sourcemodel.pos<span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"> = positions;
</span><font face="Menlo, Monaco, Consolas, Courier New, monospace"><span style="white-space:pre-wrap">template = ft_prepare_sourcemodel(cfg);
</span></font><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">cfg = [];
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.method =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'basedonmni'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.template = ft_convert_units(</span>template.sourcemodel<span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">,
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'mm'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">);</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.nonlinear
= </span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'yes'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(0,128,19)">% use non-linear normalization</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.mri
= mri_realigned;</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">sourcemodel = ft_prepare_sourcemodel(cfg);</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><font color="#008013">% Prepare head model using single-shell method
</font></span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg = [];
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.output =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'brain'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span>segmentedmri<span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"> = ft_volumesegment(cfg, mri_realigned);
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg = [];
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.method =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'singleshell'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">headmodel
= ft_prepare_headmodel(cfg, segmentedmri); </span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><font color="#008013">% Calculate means and covariances for source analysis</font></span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg
= []; </span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.covariance =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'yes'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.covariancewindow =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'all'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.channel =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'MEG'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.keeptrial =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'yes'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">tlock = ft_timelockanalysis(cfg, data); % data is preprocessed MEG data
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><font color="#008013">% Prepare leadfield model
</font></span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg = [];
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.grad = tlock.grad;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.headmodel = headmodel;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.reducerank = 2;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.channel = {</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'MEG'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">};
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.sourcemodel = sourcemodel;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(0,128,19)">% Inverse-warped template</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.normalize
= </span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'yes'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.normalizeparam = 1;</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">[lf] = ft_prepare_leadfield(cfg);
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><font color="#008013">% Run source analysis on the subject-specific inverse-warped template positions</font></span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg
= []; </span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.method =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'lcmv'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.sourcemodel = lf;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.headmodel = headmodel;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.lcmv.keepfilter =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'yes'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.lcmv.lambda =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'5%'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">cfg.lcmv.fixedori =
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(167,9,245)">'yes'</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">;</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">source
= ft_sourceanalysis(cfg, tlock);</span></div>
<div><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">nb_sources = length(source.avg.filter);
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">nb_trials = length(data.trial);
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">nb_samples = size(data.trial{1}, 2);</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">vs
= zeros(nb_sources,nb_trials,nb_samples); </span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><font color="#0e00ff">for
</font></span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">i=1:nb_sources
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">flt = source.avg.filter{i};
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(14,0,255)">if
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">isempty(flt)
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">vs(i,:,:) = NaN(nb_trials,nb_samples); % source-reconstructed timeseries
</span><span style="color:rgb(14,0,255);white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">else
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;color:rgb(14,0,255)">for
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">t=1:nb_trials
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">v = flt*data.trial{t};
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">vs(i,t,:) = v;
</span><span style="color:rgb(14,0,255);white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">end
</span><span style="color:rgb(14,0,255);white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px">end
</span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><font color="#0e00ff">end
</font></span><span style="white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><font color="#0e00ff"></font>vs = squeeze(vs);</span><span style="color:rgb(14,0,255);white-space:pre-wrap;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px"><br>
</span><span style="white-space:pre-wrap;font-size:13px"><font face="Menlo, Monaco, Consolas, Courier New, monospace"></font><font face="arial, sans-serif"><b>I have three questions:
</b>
<ol>
<li><b>Is it necessary to run ft_volumerealign before running ft_prepare_sourcemodel? The origin of the anatomical MRI does not appear to be the anterior commissure; see figure 1 below, which was produced through ft_determine_coordsys.</b></li><li><b>source.avg.pow contains very small values, on the order of 10^-47, even though the MEG data is on the order of 10^-14.</b></li><li><b>When I try to visualize the source activity, it seems totally misaligned with the anatomical MRI. See figure 2 and the code that was used to produce it below.</b></li></ol>
</font></span><font face="Menlo, Monaco, Consolas, Courier New, monospace"><span style="white-space:pre-wrap"><b>Figure 1</b></span></font></div>
<div><font face="Menlo, Monaco, Consolas, Courier New, monospace"><span style="white-space:pre-wrap"><br>
</span></font><span id="m_-8041626596201145286cid:ii_m2j9e9f81"><Screenshot 2024-10-21 at 20.56.51.png></span><br>
<br>
<b>Figure 2</b><br>
<br>
</div>
<div><span id="m_-8041626596201145286cid:ii_m2j8u6jb0"><Screenshot 2024-10-21 at 20.41.13.png></span><br>
<div><br>
</div>
<span class="gmail_signature_prefix"><font face="monospace">% Interpolate the source onto the MRI for visualization<br>
cfg = [];<br>
cfg.parameter = 'pow'; % Or 'avg.pow' depending on your data<br>
cfg.interpmethod = 'nearest';<br>
source_interp = ft_sourceinterpolate(cfg, source_placebo, mri_realigned);<br>
% Plot the source on the MRI<br>
cfg = [];<br>
cfg.method = 'ortho';<br>
cfg.funparameter = 'pow';<br>
ft_sourceplot(cfg, source_interp);<br>
</font><br>
Many thanks for reading this long email! I look forward to hearing from you.</span></div>
<div><span class="gmail_signature_prefix"><br>
</span></div>
<div><span class="gmail_signature_prefix">Best regards,</span></div>
<div><span class="gmail_signature_prefix">Kenneth Shinozuka<br>
<br>
-- </span><br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>Kenneth Shinozuka</div>
<div>Harvard College '20 | BA in Neuroscience</div>
<div>Oxford University '24 | PhD Candidate in Psychiatry</div>
<div>+1 9493028589 (US, WhatsApp)</div>
<div>+44 07572876618 (UK)</div>
</div>
</div>
</div>
</div>
</div>
</div>
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</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Kenneth Shinozuka</div><div>Harvard College '20 | BA in Neuroscience</div><div>Oxford University '24 | PhD Candidate in Psychiatry</div><div>+1 9493028589 (US, WhatsApp)</div><div>+44 07572876618 (UK)</div></div></div></div></div>