[Neuroimaging] Strange offset plotting MRIs with plot_glass_brain

bthirion bertrand.thirion at inria.fr
Tue Oct 25 14:45:06 EDT 2016

Dear Ioan -Andrei,

You images are not spatially normalized, i.e. the position in mm does 
not correspond to MNI nor to Talairach coordinates.
They at least need a non-trivial trnslation to reach one of those 
coordinate ssytem; you probably want to revise the pipeline used to 
obtain these images.


On 25/10/2016 20:29, Ioan-Andrei Bârsan wrote:
> Dear members of the PythonNeuroimaging list,
> I'm having some difficulties analyzing some MRI data using nilearn, 
> and I would be very grateful for some pointers.
> I'm using nilearn (nipype==0.12.1). Right now, I'm working on 
> visualizing some things, and later I plan on doing age predictions 
> using regression.
> However, when I plot my own data using e.g. 
> `nilearn.plotting.plot_glass_brain` I notice a strange offset. I've 
> attached a screenshot showing what happens. This does not happen when 
> using e.g. data from the sample OASIS dataset, in which case the brain 
> aligns correctly with the template.
> Could it be that the images use different coordinate system 
> conventions? I've read about MNI vs Talairach coordinates, and how 
> they differ, but I'm not sure whether this really is the problem I'm 
> having, or how I should proceed in order to gain more information.
> My .nii files 'headers don't seem to specify what kind of coordinates 
> are being used. I've attached the contents of a sample header in case 
> there's something there that I'm missing.
> I would be very grateful for some advice. Please let me know if I 
> should provide any other information!
> Kind regards,
> Andrei Bârsan
> Screen Shot 2016-10-25 at 7.41.55 PM.png
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