How to Obtain fMRI Time Series Data with IPython?

41 views
Skip to first unread message

Tan Li Tung

unread,
Jan 19, 2022, 5:08:17 PM1/19/22
to TVB Users
Dear all,

I just started to do some research on brain data and I would like to generate some time series fMRI signals in TVB that could be manipulated through IPython. May I know in this case, is there any fMRI time series (3D image of the brain + 1D time data) dataset that is available to be access? Or is there any way that I could generate synthetic dataset from IPython interface? I would like to also know where could I get more information/resources/tutorial on this.

What I basically need is a 4D fMRI time series (3D image of the brain + 1D time data) and the corresponding functional connectivity matrix of them. From the tutorials, documentations of TVB, it looks like there are more towards the structural MRI part.

Thanks.

Best regards,
Li Tung.

WOODMAN Michael

unread,
Jan 20, 2022, 3:50:18 AM1/20/22
to TVB Users

hi


The current set of monitors doesn't support a "volumetric" fMRI monitor, but you can load the volumetric parcellation and expand the regional time series into a series of volumes.


cheers,

Marmaduke

From: tvb-...@googlegroups.com <tvb-...@googlegroups.com> on behalf of Tan Li Tung <tanl...@gmail.com>
Sent: Wednesday, January 19, 2022 11:08:17 PM
To: TVB Users
Subject: [TVB] How to Obtain fMRI Time Series Data with IPython?
 
--
You received this message because you are subscribed to the Google Groups "TVB Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to tvb-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/tvb-users/4ca39b34-4087-4125-aac1-f4ab42d8549en%40googlegroups.com.

Tan Li Tung

unread,
Jan 20, 2022, 8:15:42 PM1/20/22
to TVB Users
Hi  Marmaduke,

Thanks for the reply. May I know if there is any references/tutorial that I could get started with the method that you suggested?

Thank you.

Best,
Li Tung.

WOODMAN Michael

unread,
Jan 21, 2022, 2:56:58 AM1/21/22
to TVB Users

hi


Sorry we don't have a tutorial on it yet, as the default data set doesn't include the necessary volume I mentioned.  It's something you'd get from an anatomical pipeline, e.g. the aparc+aseg.mgz from FreeSurfer.  You might for instance process an HCP dataset with the available pipelines and then you'd have such a volume mapping along with empirical fMRI to compare with.


cheers,

Marmaduke

Sent: Friday, January 21, 2022 2:15:41 AM
To: TVB Users
Subject: Re: [TVB] How to Obtain fMRI Time Series Data with IPython?
 
Reply all
Reply to author
Forward
0 new messages