Document ct_index, mr_index, pt_index from idc-index 0.12.3

Three new modality-specific acquisition parameter tables added in
idc-index-data 24.2.0: ct_index, mr_index, pt_index. All join on
SeriesInstanceUID and are fetched on demand.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: fedorov

CHANGELOG.md

@@ -5,10 +5,21 @@ All notable changes to the IDC Claude Skill are documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/),
 and this project adheres to [Semantic Versioning](https://semver.org/).
 
-## [1.6.3] - 2026-05-08
+## [1.6.3] - 2026-05-09
+
+### Added
+
+- `ct_index`, `mr_index`, `pt_index` tables (idc-index 0.12.3 / idc-index-data 24.2.0): modality-specific acquisition and reconstruction parameter indices, one row per series, all joining on `SeriesInstanceUID`
+  - `ct_index` (21 columns): pixel spacing, slice thickness, kVp, convolution kernel, tube current min/max (dose-modulated), exposure, spiral pitch, scan options
+  - `mr_index` (22 columns): field strength, scanning sequence, TE (array for multi-echo), TR, flip angle, DiffusionBValue (array for DWI), pixel bandwidth, receive coil, number of temporal positions
+  - `pt_index` (21 columns): radionuclide, injected dose, reconstruction method, decay/scatter/attenuation correction, frame duration (array for dynamic PET), number of time slices
+- SQL query patterns for all three new tables in `references/sql_patterns.md`
+- Join column entries for `ct_index`, `mr_index`, `pt_index` in `references/index_tables_guide.md` and SKILL.md
+- Parquet file entries for `ct_index.parquet`, `mr_index.parquet`, `pt_index.parquet` in `references/parquet_access_guide.md`
 
 ### Changed
 
+- Updated idc-index reference to 0.12.3
 - Clarified `download_from_selection` API: added explicit warning that it takes filter keyword arguments (not a DataFrame), comparison table vs `download_dicom_series` (which has a different first-argument order), and restructured the download example as a step-by-step query → extract UIDs → pass list flow
 - Documented `download_dicom_series` as an alternative download method with its own signature (`seriesInstanceUID` as first arg, then `downloadDir`)
 - Reduced redundancy and duplication in SKILL.md for cleaner reading

SKILL.md

@@ -5,7 +5,7 @@ license: This skill is provided under the MIT License. IDC data itself has indiv
 metadata:
     version: 1.6.3
     skill-author: Andrey Fedorov, @fedorov
-    idc-index: "0.12.2"
+    idc-index: "0.12.3"
     idc-data-version: "v24"
     repository: https://github.com/ImagingDataCommons/idc-claude-skill
 ---
@@ -145,6 +145,9 @@ Always call `client.fetch_index("table_name")` before querying any index table 
 | `contrast_index` | 1 row = 1 series with contrast info | Contrast agent metadata: agent name, ingredient, administration route (CT, MR, PT, XA, RF) |
 | `volume_geometry_index` | 1 row = 1 CT/MR/PT series | 3D volume geometry validation for single-frame CT, MR, and PT series; boolean checks for orientation, spacing, dimensions, and slice positions; composite `regularly_spaced_3d_volume` flag |
 | `rtstruct_index` | 1 row = 1 RTSTRUCT series | RT Structure Set metadata: total ROI count, ROI names, generation algorithms, interpreted types, and the referenced image series UID |
+| `ct_index` | 1 row = 1 CT series | CT acquisition/reconstruction parameters: pixel spacing, slice thickness, kVp, convolution kernel, tube current (min/max for dose-modulated), exposure, spiral pitch, scan options |
+| `mr_index` | 1 row = 1 MR series | MR acquisition/sequence parameters: field strength, scanning sequence, TE (array for multi-echo), TR, flip angle, DiffusionBValue (array for DWI), pixel bandwidth, receive coil, number of temporal positions |
+| `pt_index` | 1 row = 1 PET series | PET acquisition/reconstruction/radiopharmaceutical parameters: series type, units, decay/scatter/attenuation correction, reconstruction method, radionuclide, injected dose, frame duration (array for dynamic PET) |
 | `prior_versions_index` | 1 row = 1 DICOM series | Series that have been removed or superseded in previous IDC releases; use only to download deprecated/historical data — do not query for current data |
 
 ### Joining Tables
@@ -165,6 +168,9 @@ Always call `client.fetch_index("table_name")` before querying any index table 
 | `segmented_SeriesInstanceUID` | seg_index → index | Link segmentation to its source image series (join seg_index.segmented_SeriesInstanceUID = index.SeriesInstanceUID) |
 | `referenced_SeriesInstanceUID` | ann_index → index | Link annotation to its source image series (join ann_index.referenced_SeriesInstanceUID = index.SeriesInstanceUID) |
 | `SeriesInstanceUID` / `referenced_SeriesInstanceUID` | index, rtstruct_index | Join RTSTRUCT series to its metadata (index.SeriesInstanceUID = rtstruct_index.SeriesInstanceUID); use rtstruct_index.referenced_SeriesInstanceUID to find the source image series |
+| `SeriesInstanceUID` | index, ct_index | Link CT series to acquisition/reconstruction parameters |
+| `SeriesInstanceUID` | index, mr_index | Link MR series to sequence/acquisition parameters |
+| `SeriesInstanceUID` | index, pt_index | Link PET series to acquisition/radiopharmaceutical parameters |
 
 **Note:** `subjects`, `updated`, and `description` appear in multiple tables but have different meanings (counts vs identifiers, different update contexts).
 

references/index_tables_guide.md

@@ -1,6 +1,6 @@
 # Index Tables Guide for IDC
 
-**Tested with:** idc-index 0.12.2 (IDC data version v24)
+**Tested with:** idc-index 0.12.3 (IDC data version v24)
 
 This guide covers the structure and access patterns for IDC index tables: programmatic schema discovery, DataFrame access, and join column references. For the overview of available tables and their purposes, see the "Index Tables" section in the main SKILL.md.
 
@@ -130,6 +130,9 @@ Use this table to identify join columns between index tables. Always call `clien
 | `index` | `volume_geometry_index` | `index.SeriesInstanceUID = volume_geometry_index.SeriesInstanceUID` |
 | `index` | `rtstruct_index` | `index.SeriesInstanceUID = rtstruct_index.SeriesInstanceUID` |
 | `rtstruct_index` | `index` (source images) | `rtstruct_index.referenced_SeriesInstanceUID = index.SeriesInstanceUID` |
+| `index` | `ct_index` | `index.SeriesInstanceUID = ct_index.SeriesInstanceUID` |
+| `index` | `mr_index` | `index.SeriesInstanceUID = mr_index.SeriesInstanceUID` |
+| `index` | `pt_index` | `index.SeriesInstanceUID = pt_index.SeriesInstanceUID` |
 
 For complete query examples using these joins, see `references/sql_patterns.md`.
 

references/parquet_access_guide.md

@@ -38,6 +38,9 @@ https://storage.googleapis.com/idc-index-data-artifacts/current/release_artifact
 | `collections_index.parquet` | — | Collection-level metadata |
 | `analysis_results_index.parquet` | — | Derived dataset metadata |
 | `clinical_index.parquet` | ~0.2 MB | Clinical data column dictionary |
+| `ct_index.parquet` | — | CT acquisition/reconstruction parameters |
+| `mr_index.parquet` | — | MR sequence/acquisition parameters |
+| `pt_index.parquet` | — | PET acquisition/radiopharmaceutical parameters |
 | `prior_versions_index.parquet` | — | Series from previous IDC releases |
 
 **Note:** the main index file is named `idc_index.parquet`, not `index.parquet`. Reference it with an alias in SQL queries (e.g., `FROM read_parquet(...) AS index`).

references/sql_patterns.md

@@ -1,6 +1,6 @@
 # SQL Query Patterns for IDC
 
-**Tested with:** idc-index 0.12.1 (IDC data version v24)
+**Tested with:** idc-index 0.12.3 (IDC data version v24)
 
 Quick reference for common SQL query patterns when working with IDC data. For detailed examples with context, see the "Core Capabilities" section in the main SKILL.md.
 
@@ -14,6 +14,7 @@ Load this guide when you need quick-reference SQL patterns for:
 - Linking imaging data to clinical data
 - Filtering by 3D volume geometry validity (volume_geometry_index)
 - Finding RT Structure Set series and ROI metadata (rtstruct_index)
+- Filtering by CT/MR/PET acquisition parameters (ct_index, mr_index, pt_index)
 
 For table schemas, DataFrame access, and join column references, see `references/index_tables_guide.md`.
 
@@ -277,6 +278,84 @@ client.sql_query("""
 """)
 ```
 
+## Modality Acquisition Parameters
+
+`ct_index`, `mr_index`, and `pt_index` (added in idc-index 0.12.3) expose acquisition and reconstruction parameters for CT, MR, and PET series. All join on `SeriesInstanceUID`. Dose-modulated CT acquisitions have `_min`/`_max` columns for tube current, exposure, and exposure time.
+
+```python
+client.fetch_index("ct_index")
+client.fetch_index("mr_index")
+client.fetch_index("pt_index")
+
+# CT: thin-slice series (≤2mm) with standard reconstruction
+client.sql_query("""
+    SELECT i.collection_id, i.SeriesInstanceUID, i.BodyPartExamined,
+           c.SliceThickness, c.ConvolutionKernel, c.KVP
+    FROM index i
+    JOIN ct_index c ON i.SeriesInstanceUID = c.SeriesInstanceUID
+    WHERE c.SliceThickness <= 2.0
+      AND c.ConvolutionKernel IS NOT NULL
+    LIMIT 10
+""")
+
+# CT: dose-modulated acquisitions (tube current varies across slices)
+client.sql_query("""
+    SELECT i.collection_id, c.SeriesInstanceUID,
+           c.XRayTubeCurrent_min, c.XRayTubeCurrent_max, c.SliceThickness
+    FROM ct_index c
+    JOIN index i ON c.SeriesInstanceUID = i.SeriesInstanceUID
+    WHERE c.XRayTubeCurrent_min != c.XRayTubeCurrent_max
+    LIMIT 10
+""")
+
+# MR: DWI series (have non-null DiffusionBValue) at 3T
+client.sql_query("""
+    SELECT i.collection_id, i.SeriesInstanceUID, i.SeriesDescription,
+           m.MagneticFieldStrength, m.DiffusionBValue
+    FROM index i
+    JOIN mr_index m ON i.SeriesInstanceUID = m.SeriesInstanceUID
+    WHERE m.DiffusionBValue IS NOT NULL
+      AND m.MagneticFieldStrength >= 2.9
+    LIMIT 10
+""")
+
+# MR: multi-echo series (EchoTime stored as array with multiple values)
+client.sql_query("""
+    SELECT i.collection_id, i.SeriesInstanceUID,
+           m.EchoTime, m.EchoTrainLength, m.ScanningSequence
+    FROM index i
+    JOIN mr_index m ON i.SeriesInstanceUID = m.SeriesInstanceUID
+    WHERE m.EchoTrainLength > 1
+    LIMIT 10
+""")
+
+# PET: FDG studies with specific reconstruction method
+client.sql_query("""
+    SELECT i.collection_id, i.SeriesInstanceUID,
+           p.RadionuclideCodeMeaning, p.ReconstructionMethod,
+           p.Units, p.DecayCorrection
+    FROM index i
+    JOIN pt_index p ON i.SeriesInstanceUID = p.SeriesInstanceUID
+    WHERE p.RadionuclideCodeMeaning LIKE '%fluorodeoxyglucose%'
+    LIMIT 10
+""")
+
+# PET: dynamic acquisitions (ActualFrameDuration is array with multiple values)
+client.sql_query("""
+    SELECT i.collection_id, i.SeriesInstanceUID,
+           p.NumberOfTimeSlices, p.ActualFrameDuration
+    FROM index i
+    JOIN pt_index p ON i.SeriesInstanceUID = p.SeriesInstanceUID
+    WHERE p.NumberOfTimeSlices > 1
+    LIMIT 10
+""")
+```
+
+Key columns by table (use `client.indices_overview["ct_index"]["schema"]` for the full list):
+- **ct_index**: `SliceThickness`, `KVP`, `ConvolutionKernel`, `SpiralPitchFactor`, `XRayTubeCurrent_min/max`, `Exposure_min/max`, `PixelSpacing_row_mm/col_mm`, `Rows`, `Columns`
+- **mr_index**: `MagneticFieldStrength`, `ScanningSequence`, `SequenceVariant`, `MRAcquisitionType`, `EchoTime` (array), `RepetitionTime`, `FlipAngle`, `DiffusionBValue` (array), `NumberOfTemporalPositions`, `ReceiveCoilName`
+- **pt_index**: `RadionuclideCodeMeaning`, `Radiopharmaceutical`, `RadionuclideTotalDose`, `ReconstructionMethod`, `DecayCorrection`, `AttenuationCorrectionMethod`, `ActualFrameDuration` (array), `NumberOfTimeSlices`
+
 ## Resources
 
 - `references/index_tables_guide.md` for table schemas, DataFrame access, and join column references