ENH: extract ROI time series

[JD-Zhu]

1. MNI305to152.py: utility to help read out anatomical labels from source localisation results.
2. traditional_source_analysis_and_ROIs.py: run source analysis and save the STCs, then extract source timecourses from predefined ROIs.

[JD-Zhu]

Hi @larsoner ,

I think I'm still having some trouble with the volumetric version of the HCPMMP1 atlas. The label names load correctly when using the proper LUT file, but I still run into a problem when trying to use these labels with mne.extract_label_time_course(). Apparently the label name cannot be found in the atlas even though it shows up in the list:

Does the custom lut file need to be supplied to mne.extract_label_time_course()? I checked the documentation but couldn't find a way to do so.

Thanks in advance for any advice.

[larsoner]

Does the custom lut file need to be supplied to mne.extract_label_time_course()? I checked the documentation but couldn't find a way to do so.

Not exactly, this one is a bit tricky -- unpacking the extract_label_time_course docs:

It looks like you have passed a two-element tuple, the secend element being a list of str. Following the hint to look at setup_volume_source_space, you'll see this note about labels:

You are in the "use of other atlases" part, so instead of passing a list of str you need to pass a dict whose keys are the volume label names and the values are integer IDs used in the atlas. You should be able to get those integer IDs from your custom LUT. Does that make sense?

[JD-Zhu]

You are in the "use of other atlases" part, so instead of passing a list of str you need to pass a dict whose keys are the volume label names and the values are integer IDs used in the atlas. You should be able to get those integer IDs from your custom LUT. Does that make sense?

All works now - thank you!