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Visualization QC reports #32

Merged
merged 3 commits into from
Feb 23, 2021
Merged

Visualization QC reports #32

merged 3 commits into from
Feb 23, 2021

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akhanf
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@akhanf akhanf commented Feb 1, 2021

This PR adds visualization quick-checks for the HTML report, using some nilearn code adapted from the snakedwi workflow.

  • vis_regqc.py: plots edge contours from flo image over the ref image. Currently used to QC the T1w to CIT template registration
  • vis_dseg.py: plots orthoslice of bg img and overlaid semi-transparent segmentation. Currently used to QC the subfield seg in cropT1w space
  • gen_volume_tsv.py: uses pandas and nibabel to create a df and write subject subfield volumes to tsv
  • plot_subj_subfields.py: uses a tsv of subfield volumes to plot line plots (lh and rh) for a subject

The plotting scripts can be used generally for any other images in the workflow as needed.

I am placing all the QC png files in the work/ folder, and the TSV in the subject results folder.

To do:

  • add python code to merge the subject subfield TSVs (this had been created already, just need to integrate it into the workflow -- I plan on making this rule the group analysis level, since it aggregates over subjects)

@akhanf akhanf merged commit c77eb5f into master Feb 23, 2021
@akhanf akhanf deleted the visqc branch February 23, 2021 18:33
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