MicroDicom NIH CXR Reader Adjudication
Domain: health_medicine — Clinical Diagnostics & Imaging

Summary: Adjudicate between two competing reader annotations for a 9-case chest X-ray cohort in a Windows MicroDicom workflow, then save three cohort TSV outputs (adjudicated boxes, adjudication log, final impressions).

Task prompt:
You are a radiology adjudicator working in a Windows desktop environment.

Your task is to adjudicate between two competing reader annotations for a cohort of 9 chest X-ray studies and save the final cohort outputs.

Files and tools:
- DICOM viewer launcher: `base\software\launch_mdicom.cmd`
- Cohort instructions: `base\input\adjudication_rules.md`
- Case manifest: `base\input\case_manifest.tsv`
- Reader A draft annotations: `base\input\reader_a_annotations.tsv`
- Reader B draft annotations: `base\input\reader_b_annotations.tsv`
- Clinical notes directory: `base\input\clinical_notes`
- DICOM cases directory: `base\input\dicom_cases`
- Output directory: `base\output`

What you must do:
1. Read `adjudication_rules.md` and `case_manifest.tsv`.
2. Use the case-specific clinical notes as context.
3. Launch MicroDicom from the provided launcher.
4. For each case in the manifest, open the listed DICOM file in MicroDicom.
5. Compare the candidate reader boxes from `reader_a_annotations.tsv` and `reader_b_annotations.tsv` against the image.
6. Choose the better-supported reader result for each case.
7. Save exactly these UTF-8 tab-delimited files under `base\output`:
   - `base\output\adjudicated_boxes.tsv`
   - `base\output\adjudication_log.tsv`
   - `base\output\final_impressions.tsv`

Required schemas:
- `adjudicated_boxes.tsv`: `case_id`, `selected_reader`, `final_x`, `final_y`, `final_width`, `final_height`
- `adjudication_log.tsv`: `case_id`, `selected_reader`, `disagreement_type`, `resolution_basis`
- `final_impressions.tsv`: `case_id`, `final_finding_label`, `final_impression_label`

Task constraints:
- `selected_reader` must be either `reader_a` or `reader_b`
- `disagreement_type` must be `box_disagreement`
- `final_finding_label` must be `Atelectasis`
- `final_impression_label` must be `positive_for_atelectasis`

The agent must:
Read the cohort instructions in `input/adjudication_rules.md`.
Read `input/case_manifest.tsv` to enumerate the 9 cases.
Use the case-specific clinical notes under `input/clinical_notes/` as context.
Launch MicroDicom via `software/launch_mdicom.cmd`.
For each case, open the DICOM in MicroDicom and compare the two candidate reader boxes.
Choose the better-supported reader for each case.
Save `output/adjudicated_boxes.tsv`, `output/adjudication_log.tsv`, and `output/final_impressions.tsv` with the required UTF-8 tab-delimited schemas.

Software: MicroDicom DICOM Viewer

Input files:
name: adjudication_rules.md
format: markdown
description: high-level cohort adjudication policy and required label vocabulary
name: case_manifest.tsv
format: TSV
description: 9-case manifest enumerating the cohort cases
name: reader_a_annotations.tsv
format: TSV
description: candidate bounding boxes from reader A
name: reader_b_annotations.tsv
format: TSV
description: candidate bounding boxes from reader B
name: clinical_notes/
format: text directory
description: per-case clinical note files referenced by the manifest
name: dicom_cases/
format: DICOM directory
description: per-case chest radiograph DICOM files referenced by the manifest