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This commit updates seven notebooks to reflect the transition from using NBIA to NCI Imaging Data Commons (IDC) for accessing public DICOM data. Changes included: - Replaced `tcia_utils` with `idc-index` for querying and downloading. - Replaced `nbia.getSharedCart()` calls with hardcoded SeriesInstanceUID lists. - Updated reporting logic to use pandas on `idc_client.index`. - Added notes regarding restricted collections moving to NCI General Commons. - Implemented `seg_index` queries to find referenced image series. Affected notebooks: 1. TCIA_Series_UID_Report.ipynb 2. CPTAC/CPTAC.ipynb 3. TCGA/TCGA_Clinical.ipynb 4. TCIA_Segmentations.ipynb 5. TCIA_Image_Visualization_with_itkWidgets.ipynb 6. TCIA_RTStruct_SEG_Visualization_with_itkWidgets.ipynb 7. TCIA_STL_Visualization_with_itkWidgets.ipynb Co-authored-by: kirbyju <2379527+kirbyju@users.noreply.github.com>
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Updated seven notebooks to transition from NBIA to IDC. Refined the note for restricted collections to reflect they have moved to the Cancer Research Data Commons with different access mechanisms. Replaced shared carts with hardcoded UID lists and used idc-index for DICOM data access. Co-authored-by: kirbyju <2379527+kirbyju@users.noreply.github.com>
…iewer This commit refines the migration of seven notebooks to IDC by: - Using `seg_index` to lookup `segmented_SeriesInstanceUID` for pairing images with segmentations (RTSTRUCT/SEG). - Replacing all occurrences of `simpleDicomViewer` with the IDC OHIF viewer embedded via `IFrame`. - Updating examples to use `SEG` modality where `seg_index` lookup is demonstrated. - Ensuring restricted access notes use the refined wording about Cancer Research Data Commons. - Using pandas operations on `idc_client.index` for reporting. Affected notebooks: 1. TCIA_Series_UID_Report.ipynb 2. CPTAC/CPTAC.ipynb 3. TCGA/TCGA_Clinical.ipynb 4. TCIA_Segmentations.ipynb 5. TCIA_Image_Visualization_with_itkWidgets.ipynb 6. TCIA_RTStruct_SEG_Visualization_with_itkWidgets.ipynb 7. TCIA_STL_Visualization_with_itkWidgets.ipynb Co-authored-by: kirbyju <2379527+kirbyju@users.noreply.github.com>
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Mention this in the summary instead of its own section. "Restricted access have moved to the Cancer Research Data Commons and have different access mechanisms than the ones described in this notebook. Please see https://www.cancerimagingarchive.net/nih-controlled-data-access-policy/ for more details."
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Download an example manifest from TCIA instead of just using two series UIDs. https://www.cancerimagingarchive.net/wp-content/uploads/EAY131-DA-RAD_v01_20260216.tcia is a good one. This nbia.manifestToList() function is just removing the first 6 lines of header information and then the rest of the tcia file will be one Series Instance UID per line.
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Migrated seven notebooks from using NBIA/tcia_utils to NCI Imaging Data Commons (IDC) using idc-index. Replaced shared carts with hardcoded UIDs and updated restricted access status.
PR created automatically by Jules for task 12318540016014198590 started by @kirbyju