[Neuroimaging] Time series per voxel

[Ariel Rokem]

Nitime's time_series_from_file might also do what you want:

http://nipy.org/nitime/api/generated/nitime.fmri.io.html#nitime.fmri.io.time_series_from_file

Hope that helps,

Ariel


On Sat, Apr 28, 2018 at 3:10 PM, Gael Varoquaux <
gael.varoquaux at normalesup.org> wrote:

> In that case, the simplest thing might be to use nilearn's NiftiMasker,
> which does pretty much this:
> http://nilearn.github.io/manipulating_images/masker_objects.html
>
> Gaël
>
> 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
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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