Generate CIFTI and TSV versions of coverage, timeseries, and correlation files #785
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tsalo
changed the title
Should play nicely with PennLINC#782.
I needed to squeze the atlas_arr from 2D to 1D.
This was referenced Feb 3, 2023
tsalo
commented
Feb 4, 2023
Codecov ReportBase: 71.24% // Head: 71.42% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## main #785 +/- ##
==========================================
+ Coverage 71.24% 71.42% +0.18%
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Files 73 74 +1
Lines 6544 6562 +18
==========================================
+ Hits 4662 4687 +25
+ Misses 1882 1875 -7
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
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@mattcieslak I think this is finally ready to review. |
mattcieslak
reviewed
Feb 6, 2023
| ) | ||
| n_voxels_in_masked_parcels = sum_masker_masked.fit_transform(atlas_img_bin) | ||
| n_voxels_in_parcels = sum_masker_unmasked.fit_transform(atlas_img_bin) | ||
| parcel_coverage = np.squeeze(n_voxels_in_masked_parcels / n_voxels_in_parcels) | ||
| coverage_thresholded = parcel_coverage < coverage_threshold | ||
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| n_nodes = coverage_thresholded.size | ||
| n_nodes = len(node_labels) | ||
| n_found_nodes = coverage_thresholded.size |
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I've never seen .size used this way before.
Looks like there's one parcel in the 1000-parcel atlas with ~0.5 coverage. Is getting NaNed out in the timeseries file, but checking the value in the coverage file resulted in a mismatch.
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Going to merge. The file changes will be a drop in the bucket of the git history. |
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Closes #555 and closes #777. Supercedes #559 and #783.
Changes proposed in this pull request
--ciftiflag, generate and write out tsv versions of the coverage, timeseries, and correlation files for each atlas.CiftiPrepareForParcellationandCiftiCorrelationinterfaces.Documentation that should be reviewed