Time series data for each ROI of an atlas?

I’m looking to get time series data (average bold over time) across every ROI in an atlas… The only option I’m finding is creating masks from each ROI and running separate time series analysis for each individual ROI. The atlases I’m using have ~160 ROIs so while possible, this probably isn’t the best option.

I feel like there’s definitely a toolbox/built in command of some sort that would do this, I’m just not finding it. Thanks in advance!!


nilearn should have the functionality you are looking for (if you like python!).


Ahoi hoi,

maybe @danjgale’s new tool nii-masker might be helpful?

Cheers, Peer

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Here is a another Python option, this one from the nitime library: https://github.com/nipy/nitime/blob/master/nitime/fmri/io.py#L15, using average=True

Yet another option (nipype style): https://github.com/poldracklab/niworkflows/blob/994dd2dcdc8811c6c2fd27f85c195d0bff5412c8/niworkflows/interfaces/images.py#L668

This is exactly what I needed. I knew there was something out there. Thank you!!