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Use NaNs for low-coverage parcels #783

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@tsalo tsalo commented Jan 31, 2023

Closes #777.

Changes proposed in this pull request

  • Create interface to replace time series of zeros (i.e., parcels with bad coverage) in the parcellated CIFTI files with NaNs. It also replaces the correlation values for those parcels (assuming they're in the same order in the data array) with NaNs.
  • Use a time series of NaNs for bad parcels in the parcellated NIFTI results as well.

Documentation that should be reviewed

None.

@tsalo tsalo added enhancement New feature or request breaking-change PRs that change results or interfaces. labels Jan 31, 2023
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codecov bot commented Jan 31, 2023

Codecov Report

Base: 70.31% // Head: 70.45% // Increases project coverage by +0.14% 🎉

Coverage data is based on head (ef958b2) compared to base (39f949e).
Patch coverage: 100.00% of modified lines in pull request are covered.

❗ Current head ef958b2 differs from pull request most recent head 4671c5e. Consider uploading reports for the commit 4671c5e to get more accurate results

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #783      +/-   ##
==========================================
+ Coverage   70.31%   70.45%   +0.14%     
==========================================
  Files          71       71              
  Lines        6465     6496      +31     
==========================================
+ Hits         4546     4577      +31     
  Misses       1919     1919              
Impacted Files Coverage Δ
xcp_d/interfaces/connectivity.py 100.00% <100.00%> (ø)
xcp_d/interfaces/prepostcleaning.py 96.34% <100.00%> (+0.48%) ⬆️
xcp_d/workflows/connectivity.py 100.00% <100.00%> (ø)

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tsalo commented Jan 31, 2023

I just want to write a test or two that explicitly check for NaNs before merging. Stuck on this whole get_node thing though.

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tsalo commented Feb 3, 2023

Closing in favor of #785.

@tsalo tsalo closed this Feb 3, 2023
@tsalo tsalo deleted the nan-out-parcels branch June 26, 2023 15:07
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Ensure that zeroed-out time series/correlation coefficients are set to NaNs
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