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<p>Dear Cristophe,</p>
<p>I indeed only have the SPM.mat and have no access to the map that
you have mentioned. I did, however, revisit documentation and
realized that I was misinterpreting the some of the information
provided with the SPM.mat, and built the 3D array just like you
recommended and it indeed worked.</p>
<p>Thank you very much for your help!</p>
<p>Best Regards,</p>
<p>Ruben Branco<br>
University of Lisbon<br>
NLX - Natural Language and Speech Group, Department of Informatics<br>
Faculdade de Ciências</p>
<br>
<div class="moz-cite-prefix">On 04/03/2018 02:23 PM, Christophe
Pallier wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CALyk9bysgyX7rv1eHoj=xAwiMrYVRUxO_qkih1wnxA3aOmnesg@mail.gmail.com">
<div dir="ltr">
<div>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.<br>
<br>
</div>
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. <br>
<div>
<div><br>
</div>
<div>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.<br>
</div>
<div>Then, once you have the image, you will be able to use
plot_glass_brain.<br>
<br>
</div>
<div>Hope this helps and is not too off the mark. <br>
</div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Apr 3, 2018 at 3:03 PM, Ruben
Branco <span dir="ltr"><<a
href="mailto:ruben.branco@di.fc.ul.pt" target="_blank"
moz-do-not-send="true">ruben.branco@di.fc.ul.pt</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
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!<br>
<br>
Thank you so much for your time,<br>
<br>
Ruben Branco<br>
University of Lisbon<br>
NLX - Natural Language and Speech Group, Department of
Informatics<br>
Faculdade de Ciências<br>
<br>
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</div>
<br>
<br clear="all">
<br>
-- <br>
<div class="gmail_signature" data-smartmail="gmail_signature">--<br>
Christophe Pallier <<a href="mailto:christophe@pallier.org"
target="_blank" moz-do-not-send="true">christophe@pallier.org</a>><br>
INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,<br>
91191 Gif-sur-Yvette Cedex, France<br>
Tel: 00 33 1 69 08 79 34<br>
Personal web site: <a href="http://www.pallier.org"
target="_blank" moz-do-not-send="true">http://www.pallier.org</a><br>
Lab web site: <a href="http://www.unicog.org" target="_blank"
moz-do-not-send="true">http://www.unicog.org</a><br>
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