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Hi Vitória,
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<div class="">To me it looks as if most of the stuff you describe works as expected, i.e. it works well or it gives funny results, apart from the non-linear normalisation. The extremely distorted warped grid points may be due to the patient’s anatomical being
pathological, causing the normalisation to converge to a very strange solution.</div>
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<div class="">Now, with respect to the plotting/interpolation: if the coordinate systems of the objects you are overlaying don’t match, you get funny results. This is the case for the sourceplot with the surface method (where the default cortical surface is
in MNI-RAS), and your functional image is in CTF’s ALS, as well as for the sourceplot with the ortho method, using the blurry template from SPM (which is also in MNI-RAS). If you want these to match up, you could replace the source positions in your functional
image with the ones from the standard grid, because you assume topological equivalence as per the inverse warping strategy applied in the creation of the beamformer grid.</div>
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<div class="">So, long story short: it seems that your source analysis just went fine, but you are confused by the different coordinate systems.</div>
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<div class="">Best,</div>
<div class="">JM</div>
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<div class="">On 13 Jun 2016, at 11:02, Vitoria Piai <<a href="mailto:v.piai.research@gmail.com" class="">v.piai.research@gmail.com</a>> wrote:</div>
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<div class="">Hi Cris, </div>
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<div class="">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 class="">Any thoughts anyone?</div>
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<div class="">Thanks again</div>
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<div class="gmail_quote">On 12 June 2016 at 13:55, Cristiano Micheli <span dir="ltr" class="">
<<a href="mailto:michelic72@gmail.com" target="_blank" class="">michelic72@gmail.com</a>></span> wrote:<br class="">
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<div dir="ltr" class="">Dear Vitoria
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<div class="">I had the same problem when I tried to coregister functional and anatomical data without transitioning through a head-referenced coordinates system.</div>
<div class="">I solved the problem by using ft_volumerealign and selecting comparable anatomical fiducials for different subjects (nasion, left, right,..) BEFORE volume normalization.</div>
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<div class="">Maybe a hint towards the solution?</div>
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<div class="">Cheers</div>
<div class="">Cris</div>
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<div class="h5">On Sat, Jun 11, 2016 at 8:50 PM, Vitória Piai <span dir="ltr" class="">
<<a href="mailto:v.piai.research@gmail.com" target="_blank" class="">v.piai.research@gmail.com</a>></span> wrote:<br class="">
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<div text="#000000" bgcolor="#FFFFFF" class="">Hi everyone, <br class="">
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I was hoping someone could help me figure out where my source analysis is going wrong.
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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 class="">
mri_reslice = ft_volumereslice([], mri);<br class="">
segmentedmri = ft_volumesegment([], mri_reslice);<br class="">
This seems to be working:<br class="">
<span id="cid:part1.00000907.02010104@gmail.com"><bfejiccb.png></span><br class="">
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Plotting headmodel and sensors, it looks like they are aligned:<br class="">
<span id="cid:part2.03070600.04020506@gmail.com"><jidhfdhd.png></span><br class="">
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 class="">
<span id="cid:part3.01010008.01070904@gmail.com"><ebfighdf.png></span><br class="">
With linear transformation, things look better:<br class="">
<span id="cid:part4.02060106.03040100@gmail.com"><ehffjdea.png></span><br class="">
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 class="">
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Then, the next issue is this result when projecting the source to the surface:<br class="">
<span id="cid:part5.07080201.03090704@gmail.com"><dffeehgc.png></span><br class="">
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 class="">
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 class="">
<span id="cid:part6.06000104.05000506@gmail.com"><dcigdbdi.png></span><br class="">
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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 class="">
<br class="">
Thanks very much for any kind of help!<br class="">
Vitoria<br class="">
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