[Neuroimaging] Troubles with plotting of data from fMRI

[Christophe Pallier]

If I understand correctly, you do not have the map as an image (analyze:
img, hdr, ot nifti: nii), but only the values of a stat for suprathreshold
voxels as a series of triplets (coordinates) and values.

It looks like you only have the SPM.mat file but it would be nicer to have
the spmT*.{img,hdr} and con*.{img,hdr} files. Check first if you can have
those.

If you only have the SPM.mat file, you could create a Niftiimage by
creating a 3D numpy array and filling the voxels with the values.
Then, once you have the image, you will be able to use plot_glass_brain.

Hope this helps and is not too off the mark.


On Tue, Apr 3, 2018 at 3:03 PM, Ruben Branco <ruben.branco at di.fc.ul.pt>
wrote:

> 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
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>



-- 
--
Christophe Pallier <christophe at pallier.org>
INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,
91191 Gif-sur-Yvette Cedex, France
Tel: 00 33 1 69 08 79 34
Personal web site: http://www.pallier.org
Lab web site: http://www.unicog.org
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