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

[Vitória Piai]

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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