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

[Vitoria Piai]

Hi Cris,

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.
Any thoughts anyone?

Thanks again

On 12 June 2016 at 13:55, Cristiano Micheli <michelic72 at gmail.com> wrote:

> 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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>> fieldtrip at donders.ru.nl
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>>
>
>
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