Plotting one Activation in One ROI in Schaefer Atlas using Nilearn

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1

Hi,

I was wondering if anyone has any insight into an issue I’ve been having.

I am extracting the mean intensity under certain contrast conditions during an fMRI task. These mean intensities are being taken using specific ROIs (i.e., left DLPFC, right insula, right dACC) from the 2018 Schaefer atlas (400 parcelations, 17 networks, 2mm resolution). I am able to successfully do this using nilearn, however I am struggling to actually plot the activation in only the ROIs of interest.

When I use plotting.plot_rois it will plot the activation across the whole brain. I want to be able to show only the activation in the selected ROI from the atlas.

I tried making a mask for my ROIs by importing the Schaefer atlas into FSL, however, it will not recognize the file as an atlas (it only comes in nii.gz format, not xml).

Does anyone have any advice or suggestions?
Thanks!
Meg

2

Hi,

You need to create a mask for the ROIs of interest using the Schaefer atlas. You can do this programmatically using Nilearn.

3

Hi,
Sorry for the late reply.
What you can do is either to create a mask for the region only, using the math_img function in Nilearn.
Or you can simply zero out the values for all the regions that are of no interest to you, once you have obtain the regions means.
Does that make sense ?
Best,
Bertrand