upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/imaging-data-commons/references/cli_guide.md

@@ -2,9 +2,9 @@
 title: "idc-index Command Line Interface Guide"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/imaging-data-commons/references/cli_guide.md
-upstream_sha: 9c9bd2e9
-imported_at: 2026-06-27
+upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/d661d27e/skills/imaging-data-commons/references/cli_guide.md
+upstream_sha: d661d27e
+imported_at: 2026-08-11
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -17,9 +17,8 @@ The `idc-index` package provides command-line tools for downloading DICOM data f
 
 ## Installation
 
-```bash
-pip install --upgrade idc-index
-```
+Needs `idc-index` installed — run `python scripts/check_version.py`, which reports the installed
+version and prints the install command for the interpreter you are running.
 
 After installation, the `idc` command is available in your terminal.
 
@@ -63,6 +62,22 @@ idc download manifest.txt --download-dir ./data
 
 ### Directory Template Variables
 
+The same templates apply in Python, where the argument is `dirTemplate=` rather than the
+`--dir-template` flag. The default is
+`%collection_id/%PatientID/%StudyInstanceUID/%Modality_%SeriesInstanceUID`:
+
+```python
+# Simplified hierarchy (omit StudyInstanceUID level)
+client.download_from_selection(
+    downloadDir="./data",
+    collection_id="tcga_luad",
+    dirTemplate="%collection_id/%PatientID/%Modality"
+)
+# Results in: ./data/tcga_luad/TCGA-05-4244/CT/
+
+# dirTemplate="" disables the hierarchy, writing every file straight into downloadDir
+```
+
 Use these variables in `--dir-template` to organize downloads:
 
 - `%collection_id` - Collection identifier