[FieldTrip] help diagnosing issues with source analysis (pathological brain)

[Cristiano Micheli]

Dear Vitoria

I had the same problem when I tried to coregister functional and anatomical
data without transitioning through a head-referenced coordinates system.
I solved the problem by using ft_volumerealign and selecting comparable
anatomical fiducials for different subjects (nasion, left, right,..) BEFORE
volume normalization.

Maybe a hint towards the solution?

Cheers
Cris


On Sat, Jun 11, 2016 at 8:50 PM, Vitória Piai <v.piai.research at gmail.com>
wrote:

> Hi everyone,
>
> I was hoping someone could help me figure out where my source analysis is
> going wrong.
> 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
> mri_reslice             = ft_volumereslice([], mri);
> segmentedmri = ft_volumesegment([], mri_reslice);
> This seems to be working:
>
>
> Plotting headmodel and sensors, it looks like they are aligned:
>
> 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:
>
> With linear transformation, things look better:
>
>  One of my questions is what the consequences are of using linear
> transformation for the MNI warping given the pathological nature of these
> brains.
>
> Then, the next issue is this result when projecting the source to the
> surface:
>
> 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.
> 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.
>
>
> 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?
>
> Thanks very much for any kind of help!
> Vitoria
>
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