[Neuroimaging] Time series per voxel

Gael Varoquaux gael.varoquaux at normalesup.org
Sat Apr 28 18:10:26 EDT 2018

In that case, the simplest thing might be to use nilearn's NiftiMasker,
which does pretty much this:


On Sat, Apr 28, 2018 at 09:51:11PM +0000, Dav Clark wrote:
> I'm pretty sure the OP means individual as opposed to mean over an ROI?

> So the beginning of the choose your own adventure is whether you understand
> numpy indexing. If so, you can easily grab a time series or a slice or
> whatever. Nibabel gives you the image as a numpy array, and if you're just
> getting started if encourage you to just grab each location / time series one
> at a time. See here:

> https://docs.scipy.org/doc/numpy-1.14.0/reference/arrays.indexing.html

> http://nipy.org/nibabel/gettingstarted.html

> Cheers,
> Dav

> On Sat, Apr 28, 2018, 3:42 AM Christophe Pallier <christophe at pallier.org>
> wrote:

>     What do you mean 'preprocessed'?

>     You can extract time-series from the original EPI files (although if they
>     are not corrected for movement and slice timing delays, it may not be a
>     great idea).

>     Christophe

>     On Thu, Apr 26, 2018 at 10:39 AM, Рожнов Александр Сергеевич via
>     Neuroimaging <neuroimaging at python.org> wrote:

>         Hello!

>         My name is Alexander, I am student from Russia and I am interested in
>         MRI  investigations. I am struggling with one problem which I can not
>         solve for a long. Can you help me please?

>         My aim is to obtain time series for each voxel in exact ROI. I have
>         found methods which allow me to get one time serie for one ROI, but it
>         is already preprocessed, what is not needed. Tell me please is there
>         any way to solve this problem using implemented functions?

>         Sincerely,
>         Alexander Rozhnov
>         _______________________________________________
>         Neuroimaging mailing list
>         Neuroimaging at python.org
>         https://mail.python.org/mailman/listinfo/neuroimaging
    Gael Varoquaux
    Senior Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux

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