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Thanks, Arjen!<br>
<br>
I know for sure dim and pos fields are the same as in the template
because I do copy them from the template grid. So I'll try going
back to make sure the alignment is really happening. If I can't
figure it out, I'll post some code with it.<br>
<br>
Cheers, Vitoria<br>
<br>
<div class="moz-cite-prefix">On 3/3/2016 10:18 PM, Arjen Stolk
wrote:<br>
</div>
<blockquote
cite="mid:CAAiwptSvRt7Dr3RrYFLHo=BWNBs5=Ok3mBd31Qc23RpvsZg8Lg@mail.gmail.com"
type="cite">
<div dir="ltr">Hey Vitoria,
<div><br>
</div>
<div>Hard to tell without seeing any code, but my hunch is that
the plot on the left is subject space whereas the middle is
subject spaced data plotted in MNI space. If the
sourcemodel/grid on the left is truly MNI-aligned (but the
regular spacing suggests otherwise) than it may be an instance
of forgetting to copy over the dim and pos fields from the MNI
template to the subject mri structure. You can check whether
this is case by comparing the dim and pos fields of the
template with those of the subject. They should be the same
(after alignment).</div>
<div><br>
</div>
<div>Hopefully that solves it. Otherwise you'd probably need to
provide some code.</div>
<div>Arjen</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-03-03 21:28 GMT-08:00 Vitória Piai
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:v.piai.research@gmail.com" target="_blank">v.piai.research@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi everyone, <br>
<br>
I'm working with clinical MEG data for which part of the
source pipeline has been conducted by someone else as part
of a clinical protocol. I don't have full access to what
has been done to the MRI that I'm getting, so I'm trying
to put bits and pieces of code together to arrive at a
source reconstruction. The rest of my pipeline is the
pretty standard tutorial beamforming. <br>
<br>
I was hoping someone could help me figure out where my
source analysis is going wrong by looking at this figure.
On the left, the subject's headmodel seems to be fine
(after warping to MNI). On the right, I'm plotting the
source result without interpolating with any structural
data. In the middle you see what happens when I
interpolate the source with the "single_subj_T1.nii"
structural image.<br>
It doesn't seem to be a matter of scaling (like mm to cm),
but rather it being kinda upside down + something else?
Does anyone know by looking at this whether the error
emerges because of an unsuccessful interpolation or
because something more fundamental is going wrong earlier
on? <br>
<br>
Thanks so much, <br>
Vitoria<br>
<br>
<img src="cid:part2.04020901.00060708@gmail.com" alt=""
height="311" width="1135"><br>
<br>
</div>
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