[Neuroimaging] Troubles with plotting of data from fMRI

Ruben Branco ruben.branco at di.fc.ul.pt
Tue Apr 3 09:03:56 EDT 2018

Dear all,

I was recently handed a task with a component which has to do with neuro 
imaging, completely left-field from my field, which is NLP. I have been 
trying to plot activation in the brain from fMRI data using the package 
Nilearn, but to no avail.

The data structure is in an old format, SPM99, containing an array of 
vectors, each vector having 3 integers, which are the coordinates in 
voxel space for each voxel. I also have the affinity matrix and the 
activation values for each voxel. When trying to visualize it using 
glass brain plotting, I am unsure where to include activation and 
surprisingly, without even accounting for activation values, just 
providing the voxel data and the affinity matrix yields a single line, 
which seems like the way I am providing the image only accounts for one 
slice. Despite being an SPM99 image, I have tried to convert it to Nifti 
and the same line was the output.

I was wondering whether anyone could spot the culprit in the process 
that is causing these issues and perhaps even pointing me in the right 
direction with relevant articles. The articles I have read regarding 
this issue and the specification of the Nifti format were unhelpful, 
perhaps(or definitely!) because of my inexperience with the field.

I apologize if this sounds like a very naive plead of help, it's 
something I've never have dealt with before that's for sure!

Thank you so much for your time,

Ruben Branco
University of Lisbon
NLX - Natural Language and Speech Group, Department of Informatics
Faculdade de Ciências

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