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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 registrationvis_dseg.py
: plots orthoslice of bg img and overlaid semi-transparent segmentation. Currently used to QC the subfield seg in cropT1w spacegen_volume_tsv.py
: uses pandas and nibabel to create a df and write subject subfield volumes to tsvplot_subj_subfields.py
: uses a tsv of subfield volumes to plot line plots (lh and rh) for a subjectThe 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:
group
analysis level, since it aggregates over subjects)