<div dir="ltr"><div>Hi Cris, </div><div><br></div><div>that makes sense, except that the .mri file I'm getting from the hospital should already contain the right fiducial coordinates (or so I was told by the MEG technician). Maybe the issue is that FieldTrip is not getting these coordinates right from the .mri file if I don't run it through ft_volumerealign first. </div><div>Any thoughts anyone?</div><div><br></div><div>Thanks again</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 12 June 2016 at 13:55, Cristiano Micheli <span dir="ltr"><<a href="mailto:michelic72@gmail.com" target="_blank">michelic72@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Vitoria<div><br></div><div>I had the same problem when I tried to coregister functional and anatomical data without transitioning through a head-referenced coordinates system.</div><div>I solved the problem by using ft_volumerealign and selecting comparable anatomical fiducials for different subjects (nasion, left, right,..) BEFORE volume normalization.</div><div><br></div><div>Maybe a hint towards the solution?</div><div><br></div><div>Cheers</div><div>Cris</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Sat, Jun 11, 2016 at 8:50 PM, Vitória Piai <span dir="ltr"><<a href="mailto:v.piai.research@gmail.com" target="_blank">v.piai.research@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div><div class="h5">
<div text="#000000" bgcolor="#FFFFFF">
Hi everyone, <br>
<br>
I was hoping someone could help me figure out where my source
analysis is going wrong. <br>
I have data on brain tumour patients (MRIs are from prior to tumour
resection). From the hospital (using CTF), I receive .mri files that
already have fiducial points saved as far as I was told. I then
reslice and segment the .mri file, after reading it with ft_read_mri<br>
mri_reslice = ft_volumereslice([], mri);<br>
segmentedmri = ft_volumesegment([], mri_reslice);<br>
This seems to be working:<br>
<img width="326" height="268" alt="" src="cid:part1.00000907.02010104@gmail.com"><br>
<br>
Plotting headmodel and sensors, it looks like they are aligned:<br>
<img width="180" height="135" alt="" src="cid:part2.03070600.04020506@gmail.com"><br>
If I compute the source model with MNI-warping (non-linear
transformation), I get something that doesn't seem right. I don't
know if this is because these are not normal brains to start with:<br>
<img width="229" height="172" alt="" src="cid:part3.01010008.01070904@gmail.com"><br>
With linear transformation, things look better:<br>
<img width="233" height="188" alt="" src="cid:part4.02060106.03040100@gmail.com"><br>
One of my questions is what the consequences are of using linear
transformation for the MNI warping given the pathological nature of
these brains.<br>
<br>
Then, the next issue is this result when projecting the source to
the surface:<br>
<img width="313" height="172" alt="" src="cid:part5.07080201.03090704@gmail.com"><br>
This happens regardless of whether I use the MNI-warped grid
interpolated to the MNI template, or the patient's individual grid
skipping the MNI normalisation step, interpolated to the patient's
own T1.<br>
But if I plot with 'ortho' method, then I see that the MNI-warped
and interpolated source data is misaligned, but the patient-native
space one isn't.<br>
<img width="580" height="238" alt="" src="cid:part6.06000104.05000506@gmail.com"><br>
<br>
I can't make sense of this anymore; I've been trying all kinds of
things that don't work, so I was wondering whether anyone has an
idea of what could be going on by looking at these figures. Is it an
error already at the level of alignment of the fiducials? Or is it
due to the MNI-warping? Or a combination of issues?<br>
<br>
Thanks very much for any kind of help!<br>
Vitoria<br>
</div>
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