[FieldTrip] issue at interpolation after source analysis

Vitória Piai v.piai.research at gmail.com
Fri Mar 4 17:09:01 CET 2016

Thanks, Arjen!

I know for sure dim and pos fields are the same as in the template 
because I do copy them from the template grid. So I'll try going back to 
make sure the alignment is really happening. If I can't figure it out, 
I'll post some code with it.

Cheers, Vitoria

On 3/3/2016 10:18 PM, Arjen Stolk wrote:
> Hey Vitoria,
> Hard to tell without seeing any code, but my hunch is that the plot on 
> the left is subject space whereas the middle is subject spaced data 
> plotted in MNI space. If the sourcemodel/grid on the left is truly 
> MNI-aligned (but the regular spacing suggests otherwise) than it may 
> be an instance of forgetting to copy over the dim and pos fields from 
> the MNI template to the subject mri structure. You can check whether 
> this is case by comparing the dim and pos fields of the template with 
> those of the subject. They should be the same (after alignment).
> Hopefully that solves it. Otherwise you'd probably need to provide 
> some code.
> Arjen
> 2016-03-03 21:28 GMT-08:00 Vitória Piai <v.piai.research at gmail.com 
> <mailto:v.piai.research at gmail.com>>:
>     Hi everyone,
>     I'm working with clinical MEG data for which part of the source
>     pipeline has been conducted by someone else as part of a clinical
>     protocol. I don't have full access to what has been done to the
>     MRI that I'm getting, so I'm trying to put bits and pieces of code
>     together to arrive at a source reconstruction. The rest of my
>     pipeline is the pretty standard tutorial beamforming.
>     I was hoping someone could help me figure out where my source
>     analysis is going wrong by looking at this figure. On the left,
>     the subject's headmodel seems to be fine (after warping to MNI).
>     On the right, I'm plotting the source result without interpolating
>     with any structural data. In the middle you see what happens when
>     I interpolate the source with the "single_subj_T1.nii" structural
>     image.
>     It doesn't seem to be a matter of scaling (like mm to cm), but
>     rather it being kinda upside down + something else? Does anyone
>     know by looking at this whether the error emerges because of an
>     unsuccessful interpolation or because something more fundamental
>     is going wrong earlier on?
>     Thanks so much,
>     Vitoria
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