Collection of FHIR JSON objects representing fictious patient vignettes for use in our hackathon environment, along with DICOM images that coraborate each patient's story.
The FHIR resources in this repository are provided under an MIT license. The images under the hackathon-images submodule are mostly provided under an MIT license as well. However, The exceptions to MIT Licensing apply to certain radiology images obtained from TCIA. See README for all details.
The Society for Imaging Informatics in Medicine (SIIM) is supporting the new DICOMweb and FHIR standards by creating opportunities for it's members to interact with these systems at the annual meeting, and throughout the year through it's Hackathon event, platform and dataset.
We're using images from The Cancer Imaging Archive (TCIA) and creating fictious but believable narratives that illustrate concepts common in imaging.
This project will contain FHIR JSON objects surrounding these patient narratives, as well as a Git sub-module for the DICOM images supporting these patient narratives.
During our first hackathon in 2014, we realized that in order to have a successful hackathon across multiple platforms, we need to have a cohesive, rich dataset that will allow people to build interesting applications.
In the top level directory there are directories for resources that cross patients (Medications, Practitioner, Organizations)
Also within the top level directory are a set of sub-folders for each patient. This skeleton contains a set of top-level directories that correspond with the FHIR Resources: http://www.hl7.org/implement/standards/fhir/resourcelist.html. Within these sub-folders are json FHIR documents.
Each FHIR document should have a commented header that looks like this: // filename // id: random
If set to something other than random, this will be used to create the FHIR resource.
This is not meant to be an exhaustive collection, the types are chosen based on relevance to imaging patients.
Contains DICOM images (aka part 10 files) under each patient's name, nested below are folders representing the individual studies.
These files can easily be pushed in a DICOM server, e.g. Orthanc or dcm4chee, using multiple methods, one of which is the dcm4che library (not to be confused with the dcm4chee server).
NOTE: The DICOM files are placed in a sub-module and therefore are not checked out/cloned automatically. To retrieve the files (about 1.4 GBs), either perform a recursive clone of this repository, or if already cloned, go into the hackathon-images directory and perform git submodule update. For example:
cd hackathon-images
git submodule update --init --recursivecp fhir_server.yml.dist fhir_server.ymlEdit fhir_server.yml to fit your needs.
Install dependencies for the upload script.
recommend using Poetry to interact with the pyproject.toml
poetry install --no-rootRun the script to upload all of the resources in the sub-folders.
poetry run python upload.py fhir_server.yml .You can also update only a subset of the resources by specifying a top-level directory.
poetry run python upload.py fhir_server.yml siim_andy_tcga-50-5072/DiagnosticReportFormatting and linting support
poetry run black upload.py
poetry run isort --virtual-env .venv upload.pyThere are three components to the MHD resource creation process. The create_mhd.rb script, and two ERB templates for the JSON resources. create_mhd.rb takes a single patient directory as an input, reads all of the resources for that patient, and creates DocumentReference resources for each of the DiagnosticReport and ImagingStudy resources. These are stored in subdirectories for that particular patient.
ruby create_mhd.rb <patient_folder>These can be subsequently uploaded to a FHIR server
Look in the contribute folder, which contains a python script to generate FHIR resources (Patient, ImagingStudy) from traveresed DICOM files. It can be used as per the instructions below...
pip install --no-cache-dir -r requirements.txt
python generate-fhir-from-dicom.py -d [Path to DICOM files]
The script has the option to generate dummy DiagnosticReport FHIR resources with the -r true flag.
58 yo female DOB: 04/12/1950
HPI: Had a palpable left breast mass discovered on self-breast exam. Patient was initially seen for diagnostic mammogram on 4/12/2008. Patient had a lumpectomy on 5/24/2008.
PMHx: Hypothyroidism
Allergies: NKDA
Medications: levothyroxine sodium 50mcg once daily
Lab/Radiology
DIAGNOSTIC BILATERAL 4/12/2008
Clinical History: 59 year-old female with history of left invasive ductal carcinoma (age 55) status post lumpectomy.
Technique: Bilateral CC and MLO, Left spot compression LMLO views were obtained
Findings:
LEFT BREAST: There are scattered fibroglandular densities. There are expected lumpectomy changes in the upper outer quadrant with surgical clips in place. Skin thickening is consistent with post radiation changes. No concerning masses, architectural distortions, or suspicious calcifications are identified.
RIGHT BREAST: There are scattered fibroglandular densities. No concerning masses, architectural distortions, or suspicious calcifications are identified.
Impression:
LEFT BREAST: Expected lumpectomy changes. Benign. BI-RADS 2 - Recommend routine screening in 1 year.
RIGHT BREAST: Negative. BI-RADS 1 - Recommend routine screening in 1 year.
OVERALL BI-RADS 2 (Benign)
Bilateral Breast MRI 04/19/2008
Clinical History: 59 year-old female with history of left invasive ductal carcinoma (age 55) status post lumpectomy. High-risk screening MRI exam.
Technique: Bilateral axial imaging of the breasts was obtained including T1, STIR, T1FS, and sequential T1FS+C. Digital subtraction and dynamic contrast curve analysis was performed on a separate workstation.
Findings:
LEFT BREAST: There is minimal benign background enhancement. There are expected post surgical changes in the upper outer breast. Multiple signal voids represent surgical clips in place. Skin thickening is consistent with post radiation change. There is no abnormal enhancement to indicate residual or recurrent disease. There are no morphologically abnormal axillary lymph nodes.
RIGHT BREAST: There is minimal benign background enhancement. There is no abnormal enhancement or lymphadenopathy.
Impression:
LEFT BREAST: Expected post treatment changes. Benign. BI-RADS 2. Recommend routine screening mammography in 1 year.
RIGHT BREAST: Negative. BI-RADS 1. Recommend routine screening mammography in 1 year.
OVERALL BI-RADS 2 (Benign)
Full Field Digital Left Diagnostic Mammogram 4/19/2008
Clinical History: 59 year-old female with history of left invasive ductal carcinoma (age 55) status post lumpectomy.
Technique: LML, L XCCL
Findings:
LEFT BREAST: There are scattered fibroglandular densities. There are expected lumpectomy changes in the upper outer quadrant with surgical clips in place. Skin thickening is consistent with post radiation changes. No concerning masses, architectural distortions, or suspicious calcifications are identified.
Impression:
LEFT BREAST: Expected changes status post lumpectomy and radiation. Benign. BI-RADS 2 - Recommend routine screening in 1 year.
05/24/2008 Surgical Specimen Radiograph
Clinical History: Unknown
Technique: Single surgical specimen radiograph
Findings: The surgical specimen contains an intact wire and surgical clip. No masses or calcifications are identified.
Impression:
Specimen radiograph with intact wire and surgical clip.
HPI: 60 yo male with chronic lung disease.
CT Chest with Contrast 1/1/00 at 10:04 AM
Clinical History: Abnormal chest x-ray
Comparison: Chest XR 1/1/00
Technique: Contiguous axial CT images of the chest were obtained after the administration of IV contrast material.
Findings:
The heart is normal in size. There is no pericardial effusion.
The thoracic aorta is normal in size and caliber. There is a bovine configuration of the aortic arch, a normal variant. Mild atherosclerotic changes are present in the upper abdominal aorta.
There is a 2.2 x 1.4 cm cavitary lesion in the left upper lobe (Image 30/116). Linear bandlike areas of scarring/atelectasis are present in the right upper lobe with associated bronchiectasis. Bronchiectasis is also seen in the left upper lobe. The central airways are clear. Pleural-parenchymal scarring is present at the lung apices. There is no pleural effusion.
There is no axillary, mediastinal, or hilar adenopathy. The thyroid gland is within normal limits.
The visualized portions of the upper abdomen are unremarkable. No suspicious osseous lesion is seen. There is evidence of prior trauma/deformity of the right 5th rib.
Impression:
Cavitary lesion in the left upper lobe. Differential diagnosis infectious and neoplastic disease.
Bandlike areas of atelectasis/scarring and bronchiectasis in the right upper lobe likely related to prior infection/insult.
Chest: AP View
Clinical History: Cough
Comparison: None
Findings:
The cardiomediastinal silhouette and pulmonary vasculature are within normal limits.
Linear scarring and pleural thickening are present in the right upper lobe. There is thickening of the right paratracheal stripe as well as questionable righit hillier adenopathy. A 1.6 cm nodule projects in the left upper lobe. The right costophrenic angle is effaced.
No free air beneath the hemidiaphragms. The osseous structures are grossly unremarkable.
Impression:
1.6 cm left upper lobe nodule.
Right upper lobe scarring and pleural thickening along with right pleural effusion versus scarring.
Recommendations:
CT Chest is recommended to further evaluate the above findings and impression.
CT Chest with Contrast
Clinical History: Abnormal chest x-ray
Comparison: Chest XR 1/1/00, Chest CT 10:04 AM 1/1/00
Technique: Contiguous axial CT images of the chest were obtained after the administration of IV contrast material.
Findings:
The heart is normal in size. There is no pericardial effusion.
The thoracic aorta is normal in size and calibur. There is a bovine configuration of the aortic arch, a normal variant. Mild atherosclerotic changes are present in the upper abdominal aorta.
There is a 2.1 x 1.4 cm cavitary lesion in the left upper lobe (Image 28/116). A smaller cavitary lesion is seen in the right lower lobe measuring 9 mm (Image 40/116). Linear bandlike areas of scarring/atelectasis are present in the right upper lobe with associated bronchiectasis. The central airways are clear.
There is no axillary, mediastinal, or hilar adenopathy. The thyroid gland is within normal limits.
The visualized portions of the upper abdomen are unremarkable. No suspicious osseous lesion is seen. There is evidence of prior trauma/deformity of the right 5th rib.
Impression:
Interval evolution of left upper lobe cavitary lesion in the left upper and new right lower lobe nodule. Given the rapid evolution of these cavitary lesions an infectious etiology is favored.
Unchanged bandlike areas of atelectasis/scarring and bronchiectasis in the right upper lobe likely related to prior infection/insult.
HPI: 60 yo male with history of lung adenocarcinoma.
CT Onco Lung Mass 3/30/1986
Clinical information 60 yo male with left hilar mass.
Comparison None.
Findings Lung mass Size: 5.3 x 4.0 x 4.0 cm
Location: left hilar region
Shape: Smoothly marginated
Internal consistency: homogenous, hypodense to surrounding muscle.
Local extent Pleural surface: Left lower lobe metastasis
Chest wall: No involvement.
Airway: Compression of the lingula
Vessels: Mass surrounds and nearly occludes the left inferior pulmonary artery.
Nerves: No involvement.
Regional extent Lymph nodes: AP window, and right hilar adenopathy.
Distant metastases (chest and upper abdomen): None.
Other findings Other findings: None.
Impression Left hilar mass concerning for malignancy.
Duration of fast prior to injection: 6 hours
Blood glucose prior to injection: 85 mg/dl
Scan region: Brain, Neck, Chest, Abdomen
Radiopharmaceutical: F-18 FDG 10 mCi IV
Calibration time: 4/22/1986 10:30 AM
Administration time: 4/22/1986 10:32 AM
Injection site: left antecubital fossa
Post-injection imaging delay: 60 minutes
Attenuation correction: Rod source transmission scan.
Clinical information 60 yo male with left hilar mass, evaluate for metastatic disease
Comparison Chest CT scan 3/30/1986
Findings Hypermetabolic foci: 5.0 cm hypermetabolic left hilar mass on image 162 with a maximum SUV of 3.2. 1.8 x 1.2 cm hypermetabolic AP window lymph node on image 132 maximum SUV of 2.7 There is spurious activity in the neck musculature. No contralateral hypermetabolic lesions are appreciated.
The right hilar adenopathy suspected on the prior CT scan is not seen.
Other findings: The visualized brain parenchyma is unremarkable. The soft tissues of the neck are unremarkable. The thyroid gland is unremarkable. No axillary adenopathy. No focal infiltrate. No pneumothorax. There a tiny left pleural effusion vs. pleural thickening. This is not FDG avid. The heart size is normal. No pericardial effusion.
Lack of IV contrast mildly limits evaluation of the organs in the abdomen and pelvis. The liver is unremarkable without focal lesion. The adrenals are normal. The pancreas, spleen, and kidneys are unreamarkable.
Atherosclerotic calcification is seen throughout the aorta. No abnormally dilated bowel. No suspicious retroperitoneal or mesenteric adenopathy.
There are no suspicious bony lesions.
Impression
EORTC Response Criteria: N/A - Baseline
SIIM Diagnostic Lab Leesburg, VA Tel: (555) 555-5555 Fax: (812) 353-5445
Surgical Pathology Report
Patient Name: TCGA-17-Z058. Accession #: z058path Med. Rec. #: TCGA-17-Z058 Taken: 4/25/1986 Encounter #: 000111111111 Received: 4/25/1986 Gender: M Reported: 4/26/1986 16:50 DOB: (Age: 60) Submitting Physician: REFERRING, MD Additional Physician(s): Location: ENDOSCOPY BL
Pre-Operative Diagnosis: Lingular lung mass
Post-Operative Diagnosis: Same
Specimen Received: Lingular lung bxs
Final Pathologic Diagnosis: Lingula, lung, transbronchial biopsies: Adenocarcinoma (see note)
The examination of this case material and the preparation of this report were performed by the staff pathologist. Electronically Signed by Joe Pathologist, M.D.
Signing Location: SIIM Laboratory Services, Leesburg, VA
Gross Description: Submitted in formalin as "left upper lobe-lung biopsies" are multiple fragments of light tan tissue each measuring up to 0.5 cm in greatest dimension. The entire specimen is submitted in a single cassette.
Microscopic Description: Sections of bronchial mucosa demonstrate infiltration by poorly differentiated malignant cells which form cords and some, and somewhat pale cytoplasm. Some cells have a suggestion of signet ring cell morphology. No keratinization is evident.
NOTE: This is a fictious report that was created to match the TCIA images. This is NOT the actual report for this patient.
END OF REPORT
Clinical Indication: Acute shortness of breath, elevated D-dimer. History of lung cancer. Concern for PE.
Comparison: PET/CT from 4/22/1986
Technique: Multidetector axial CT of the chest was performed after the administration of intravenous contrast in the arterial phase using a pulmonary embolus protocol.
Findings: Enteric drainage catheter courses into the stomach. Endotracheal tube terminates in the mid-thoracic trachea.
There is adequate opacification of the pulmonary vasculature to the subsegmental level without significant motion artifact. No evidence of pulmonary embolism. The main pulmonary artery and right heart are normal in size. A small pericardial effusion is present.
The thyroid and thoracic inlet are normal. No axillary lymphadenopathy. There is stable right hilar lymphadenopathy, slightly enlarged compared to the prior exam.
Emphysema again noted. Post surgical changes from interval left lower lobectomy. A large left hydropneumothorax is noted. There is diffuse bilateral septal thickening compatible with pulmonary edema. The major airways are patent.
Stable indeterminate subcentimeter enhancing lesion in the hepatic dome. Stable mildly enlarged gastrosplenic lymph node. Upper abdomen otherwise unremarkable.
Surgical defect noted in the posterior 6th rib. Osseous structures otherwise unremarkable.
Impression:
Clinical indication: Followup lung mass.
Comparison: Chest CTA from 5/5/1986
Technique: Multidetector axial CT of the chest was performed without the administration of intravenous contrast.
Findings:
Interval placement of a tracheostomy tube.
The thyroid and thoracic inlet are normal. There are no grossly enlarged axillary or mediastinal lymph nodes, however the hila are difficult to assess without the use of contrast. There is relative hyperdensity of the intraventricular septum suggestive of anemia. The heart is normal in size without significant pericardial effusion. A small hiatal hernia is present.
Stable emphysema. Post-surgical changes from left lower lobectomy again seen with persistent moderate to large subpulmonic loculated hydropneumothorax. Interval decrease in septal thickening with mild persistent septal prominence within the right lung.
Upper abdomen unremarkable given lack of IV contrast.
Stable surgical defect in the posterior left 6th rib. No suspicious osseous lesions.
Impression:
Clinical indication: History of lung adenocarcinoma, followup.
Comparison: Multiple prior CTs, the most recent from 5/31/1986
Technique: Multidetector axial CT of the chest, abdomen and pelvis was performed after the administration of intravenous contrast in the portal venous phase.
Findings:
Thorax: The thyroid and thoracic inlet are normal. There are no enlarged axillary lymph nodes. There has been interval development of an enlarged lymph node conglomerate mass within the posterior mediastinum just anterior to the descending aorta, measuring 2.8 x 4.2 cm in axial dimension (series 5, image 36). This mass anteriorly displaces and mildly narrows the left main pulmonary artery. There is no clear evidence of vascular invasion. There is stable right hilar adenopathy. A new markedly enlarged precardial lymph node is also now seen, measuring 3.3 x 1.7 cm (series 5, image 42).
There is stable severe emphysema. A 4 mm left apical nodule (series 5, image 6) appears stable. Surgical changes from prior left lower lobectomy are evident with associated pleural thickening. Interval resolution of the previously noted left hydropneumothorax. A small left lateral rim enhancing pleural collection is suspicious for infection.
No suspicious osseous lesions. The visualized soft tissues are unremarkable.
Abdomen: Punctate calcifications noted in the right hepatic lobe. Liver otherwise unremarkable. Gallbladder, pancrease, speen, and adrenal glands are normal. Bilateral renal cysts are noted. The kidneys are otherwise unremarkable with normal enhancement.
An enlarged gastrosplenic node is noted, measuring 1.3 cm in short axis dimension (series 6, image 13). The visualized bowel is within normal limits.
Impression:
Post surgical changes from left lower lobectomy.
Development of posterior mediastinal and precardial lymphadenopathy concerning for disease progression. An enlarged gastrosplenic node is nonspecific and appears grossly stable compared to CT from 4/22/1986 given differences in technique.
Small rim enhancing left pleural fluid collection concerning for infection.
HPI: 65 yo Female with recurrent right base of tongue cancer after chemotherapy and radiotherapy
CT Head and Neck with contrast 4/28/1986
Clinical information: 65 yo Female with recurrent right base of tongue cancer after chemotherapy and radiotherapy
Comparison: None.
Technique: Sequential axial CT images were obtained from the base of the brain to the thoracic inlet following the uneventful administration of intravenous contrast.
Findings: Orbits, paranasal sinuses, and skull base: Normal skull base and orbits. Mucosal thickening in both maxillary sinuses.
Nasopharynx: Normal.
Suprahyoid neck: There is a nectrotic heterogenously enhancing mass in the base of the right tongue that measures 3.0 cm x 3.7 cm (Ap versus transverse) with gas identified in the mass. No bulky local lymph nodes. No extension of the mass into the mandible, retropharyngeal or parapharyngeal space. Mild mass effect into the oropharynx.
Infrahyoid neck: Normal larynx, hypopharynx, and supraglottis.
Thyroid: Normal.
Thoracic inlet: Normal lung apices and brachial plexus.
Lymph nodes Normal. No lymphadenopathy.
Vascular structures: Normal.
Other findings: None.
Impression
5/14/1996 PET Oncologic Study
Duration of fast prior to injection: 12 hours
Blood glucose prior to injection: 100 mg/dl
Scan region: Whole body scan
Radiopharmaceutical: F-18 FDG 12.9 mCi IV
Administration time: 11:35
Post-injection imaging delay: 60 minutes
Attenuation correction: Rod source transmission scan.
Clinical information 65 yo Female with recurrent right base of tongue cancer after chemotherapy and radiotherapy
Comparison CT Head and Neck 4/28/1986. No prior comparison PET scan
Findings Hypermetabolic foci: Increased FDG uptake in the base of the tongue with max SUV of 8.4.
Physiologic uptake identified. No other areas of increased uptake.
Other findings: The lungs are clear bilaterally. No pulmonary nodules, consolidations, or pleural effusions.
No axillary, hilar, mediastinal, or paratracheal lymphadenopathy.
Heart size is normal. No pericardial effusion. Calcific coronary atherosclerosis.
The visualized osseous structures are unremarkable. No suspicious sclerotic or lytic lesions observed.
Chest wall is unremarkable.
The liver, gallbladder, pancreas, spleen and adrenal glands are within normal limits. There is no retroperitoneal or mesenteric lymphadenopathy.
The visualized loops of small bowel and large bowel are within normal limits. No free fluid or free air within the visualized abdomen.
Impression
HPI: 75 yo with lung cancer
Indication: Mass seen on chest x-ray
Comparison: None.
Procedure: CT scan of the chest was performed without intravenous contrast.
Findings: No suspicious axillary or supraclavicular adenopathy. There are several enlarged mediastinal lymph nodes including 2.7 x 2.2 cm AP window (series 3, image 22), 1.9 x 1.6 cm lower paratracheal (series 3, image 23). There are a few small right paratracheal nodes that are not enlarged by CT size criteria.
Evaluation of lung windows demonstrates a 4.4 x 3.4 cm left upper lobe mass with well circumscribed borders (series 3, image #12). A smaller daughter mass measuring 1 cm is seen on (series 3, image #18). There are no contralateral lung nodules. Emphysematous changes are seen greatest in the upper lobes. No focal infiltrate or pneumothorax. No pleural thickening or pneumothorax.
Non-contrast evaluation of the upper abdomen is unremarkable. The liver demonstrates homogenous attenuation. The adrenal glands are partially imaged, but appear within normal limits.
Evaluation of bone windows does not demonstrate suspicious lucent or sclerotic lesion.
Impression:
Exam: PET/CT Scan Whole Body
Date: 2/11/2000
Indication: Initial staging for lung cancer
Procedure: Following injection of 14.6 mCi of F-18 labeled glucose, concurrent PET CT scanning was performed. Patient also recieved 125 ml of isovue intravenously for diagnostic scanning purposes.
Findings: Oncologic Findings: Again seen is a 4.6 x 4.6 mass in the left upper lobe (series 3, iamge 78). The SUV max of the mass is 3.1.
The large AP window lymph node on (series 3, image 89) is again noted and has a maximum SUV of 1.5.
No contralateral lung nodules are identified. There is physiologic activity in both adrenal glands.
No FDG avid bone metastasis.
Other Findings: Visualized intracranial structures are unremarkable. The trachea is midline. The thyroid is unremarkable. No cervical adenopathy. The salivary glands are unremarkable.
Continued emphysematous changes in the upper lobes bilaterally. No infiltrate or pleural effusion. No pneumothorax.
The liver enhances homogenously. The spleen and pancreas are within normal limits. The kidneys are unremarkable. Visualized bowel is unremarkable. No free fluid or free air.
Extensive vascular changes are noted including AAA graft. The vessels are grossly patent.
The prostate and seminal vesicles are within normal limits. The bladder is unremarkable.
Impression:
Whole Body Tc-99m Bone Scintigraphy 2/23/2000
Indication: History of lung cancer with back pain, evaluate for bone mets
Procedure: Following intravenous administration of a standard dose of Tc-99m (not indicated in metadata) MDP a bone scan was performed.
Findings: No suspicious areas of increased or decreased uptake to suggest bony metastatic disease. Suspect bilateral first MCP degenerative change.
Impression: Negative for bony metastatic disease.
PET/CT scan whole body with IV contrast 4/19/2000
Indication: Measure response from lung cancer.
Procedure: Simultaneous PET/CT scanning was performed 1 hour and 18 minutes following intravenous administration of 14.48 mCi of FDG. Gastroview enteric contrast was administered prior to the CT scan. 125 mL of Isovue was administered intravenously at the time of the CT scan to improve diagnostic accuracy.
Findings:
Again seen is a mass in the left upper lobe (series 3, image 85). This currently measures 2.8 x 2.1 cm (previously 4.6 x 4.6 cm). The max SUV is 1.96 (previously 3.1).
The AP window adenopathy (series 3, image 85) has also decreased in size. This now measures 2.0 x 1.7 cm (previously 3.2 x 2.4 cm). The SUV max of this lesion is 1.46 (previously 1.53).
No right hilar adnenopathy. No paratracheal adenopathy. No contralateral lung lesions.
No FDG-avid metastatic disease in the abdomen or pelvis.
Other Findings: There is continued mild cardiomegaly. The liver enhances homogeneously. The pancreas is unremarkable. The esophagus and stomach are unremarkable. The spleen is within normal limits. The kidneys are unremarkable. Again seen is an aortic graft which appears patent. The celiac and superior mesenteric arteries are patent.
There is normal progression of enteric contrast. Stool is scattered throughout the colon. Scattered colonic diverticula without diverticulitis.
There is mild diffuse thickening of the anterior bladder wall.
Bone windows are unreamarkable. No sclerotic or lucent lesions are identified.
Impression: