ccna-biomarkers/ccna_ts_extraction

ccna timeseries extraction

ccna_ts_extraction's Issues

Resample template and save a temporary copy

I recently find out if the atlas and the data are in the same space, it takes a split second for LabelsMasker to run. I think it is worth resampling the template before hand.

atlas name as CLI option

#7 (comment)

Update to nilearn 0.9.x?

As title. The things we need are in release now!

Make sure the connectome / time series is fully complied with BIDS standard

See docs on derivatives:

https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html

Different denoising strategies

In my denoising project I used the load_confounds API to load a range of denoising strategy. Let me know if you think it's a good idea to implement that.

original difumo with templateflow layout

On branch https://github.com/ccna-biomarkers/ccna_ts_extraction/tree/masker_with_input_atlas

The job fails because it tries to download difumo (CC node does not have connection to internet).
Even if pre-downloaded and because the atlas-path param is already used to point to templateflow dir, this requires the atlas-path directory filled with non-templateflow files (original difumo in nilearn layout) resulting in a messy folder.

@htwangtw lmk when you have the PR to make the templateflow layout for original difumo.
OR write behind what you had in mind so I can work on it (download with tpltflow utility I suppose?).

Fix DiFuMo templateflow fetch

Seems like the templateflow fetcher does not work with DiFuMo.
To double check on another system.