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* get masks from MP-RAGE images instead * re-enable polyfit, adjust graph ylims, stop hard coding t-dimension in normalization * actions job uses new script options
…g, add institution name to report, registration QC WIP
…otype) based on zeros
… more specific, freesurfer option
output logs
ROCKETSHIP branch changed (llu-usc-script -> dev)
…aths with dynamic file retrieval, enhance error handling for missing files, update case report to include new DCE reference format, add venv reqs for ez install
…e a bunch of code blocks, add Vp for each brain region, calculate SNR for each DCE, stop excluding GE Signa and aliasing cases
…essing MNI registration
…e clarity with details for processing steps, new repo name too
…riable for Docker build, removing deprecated set-output cmd
…s for preprocessing, add cortical thickness stats to spreadsheet
…nly do organizational secrets
…r temporal cortex metrics to population report, update DICOM sort paths
Refactors the population report generation logic for clarity and maintainability, removing redundant variable resets and commented code, and consistently applying naming conventions for output metrics. Adds robust checks for subject metadata and streamlines data integration from external spreadsheets. Enhances the processing script with an explicit file-based locking mechanism to prevent concurrent data processing conflicts across machines. Updates documentation for better readability and accuracy. These changes improve robustness, reproducibility, and maintainability of the analysis pipeline.
…text location fix, nanmeans/nanmedians/nanstds for stats due to nonconvergence now resulting in NaNs, pop report refactor, wmparc stats fix now that not ignoring errors, KTRANS_MIN_THRESHOLD application to ktrans map fix, some fixes for docker (README, preprocess)
…ayers, couple fixes
…ructure, this is mostly for Docker
…-interactive, restore var from other branch that was needed
…eference KTRANS_MIN_THRESHOLD, ensure nans are dealt with in ktrans_analysis, add spreadsheet sheet for missing data, bit of improved logic in pop report and include partial failures in successes(?)
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