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4Quant / COPD-staging

Package of tools to quantify lung disease (COPD) using any number of popular medical quantifiers (PD15, LAA-x...)
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Stolz Anonymous Test Data #77

Closed drtjre closed 8 years ago

drtjre commented 8 years ago

Create a set of 3 Anonymous CT data sets with previously calculated Quantities to be used for testing.

drtjre commented 8 years ago

Anonymize 3 Stolz

Three Stolz cases are available on USBshare/StolzAnonymize.
Manually performing LungSegmentation/Quant using Fiji results in legitimate results:

PatientName (Anonymized) StudyID LungVol    PD15    LAA-950mm^3
Anonymous Sid 10007     SID10007    2.841   -858    49240.431
Anonymous Sid 10113     SID10113    3.68    -886    41568.794
Anonymous Sid 10201     SID10201    4.471   -937    390522.385

The 3 anonymized cases have been loaded into Osirix for testing with RIQAE - see below for results.

Create Table from csv-PACS:

CREATE TEMPORARY TABLE stolz3pacs USING fourquant.pacs OPTIONS (bind "YETI", username "OSIRIX", server "localhost", port "11112", path "StolzAnonymous3.csv");

where StolzAnonymous3.csv is:

Patient Name;Patient ID;Study Instance UID;Study Date;Study Description;Series Instance UID;Series Description;Result
Anonymous^Sid^10007;;;;;;;
Anonymous^Sid^10113;;;;;;;
Anonymous^Sid^10201;;;;;;;

Check table:


0: jdbc:hive2://127.0.0.1:8000/> select PatientName from stolz3pacs;
+----------------------+--+
|     PatientName      |
+----------------------+--+
| Anonymous Sid 10007  |
| Anonymous Sid 10201  |
| Anonymous Sid 10113  |
+----------------------+--+

Perform a simple Measure calculation:

This appears to produce non-zero reasonable results as expected:

select patientname,seriesDescription,runmap(fetch_dicom_imagej(studyInstanceUID,seriesInstanceUID),"Measure","") from stolz3pacs where success=true;
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.49001.30000008123113283818700000454 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20081231.103551.64 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs7121845210281147784.properties --directory emptyDir
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.54504.30000008112007153707800007751 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20081120.125332.60 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs3246684587818035570.properties --directory emptyDir
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.50021.30000008051505383531200008814 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20080515.113315.4 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs7126723019959534364.properties --directory emptyDir
+----------------------+------------------------+--------------------------------------------------+--+
|     patientname      |   seriesDescription    |                       _c2                        |
+----------------------+------------------------+--------------------------------------------------+--+
| Anonymous Sid 10007  | HWS+Thx art. 3.0 B30f  | {"Area":[262144.0],"Mean":[215.31087112426758]}  |
| Anonymous Sid 10201  | Thorax nativ 3.0 B30f  | {"Area":[262144.0],"Mean":[471.34604263305664]}  |
| Anonymous Sid 10113  | LE 3.0 B30f            | {"Area":[262144.0],"Mean":[762.6416549682617]}   |
+----------------------+------------------------+--------------------------------------------------+--+

Perform PD/LAA Quantification

Trial on "unsegmented" image data results in all values as Zero/null:

select patientname,seriesDescription,studydate,runmap(fetch_dicom_imagej(studyInstanceUID,seriesInstanceUID),"PD LAA Quantify SegmentedLung","") from stolz3pacs where success=true;
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.49001.30000008123113283818700000454 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20081231.103551.64 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs6227654999163457109.properties --directory emptyDir
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.54504.30000008112007153707800007751 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20081120.125332.60 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs4131042739232563902.properties --directory emptyDir
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.50021.30000008051505383531200008814 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20080515.113315.4 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs8837834746381452551.properties --directory emptyDir
+----------------------+------------------------+------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--+
|     patientname      |   seriesDescription    | studydate  |                                                                                                                                    _c3                                                                                                                                    |
+----------------------+------------------------+------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--+
| Anonymous Sid 10007  | HWS+Thx art. 3.0 B30f  | 20081231   | {"FOV voxels ":[8.2313216E7],"LAA-1024%":[0.0],"LAA-1024pixel^3":[0.0],"LAA-900%":[0.0],"LAA-900pixel^3":[0.0],"LAA-950%":[0.0],"LAA-950pixel^3":[0.0],"LungVol pixel^3":[0.0],"LungVol voxs":[0.0],"PD15":[0.0],"StudyID":[NaN],"sex":[NaN],"vox volume pixel^3":[1.0]}  |
| Anonymous Sid 10201  | Thorax nativ 3.0 B30f  | 20081120   | {"FOV voxels ":[4.6923776E7],"LAA-1024%":[0.0],"LAA-1024pixel^3":[0.0],"LAA-900%":[0.0],"LAA-900pixel^3":[0.0],"LAA-950%":[0.0],"LAA-950pixel^3":[0.0],"LungVol pixel^3":[0.0],"LungVol voxs":[0.0],"PD15":[0.0],"StudyID":[NaN],"sex":[NaN],"vox volume pixel^3":[1.0]}  |
| Anonymous Sid 10113  | LE 3.0 B30f            | 20080515   | {"FOV voxels ":[5.7933824E7],"LAA-1024%":[0.0],"LAA-1024pixel^3":[0.0],"LAA-900%":[0.0],"LAA-900pixel^3":[0.0],"LAA-950%":[0.0],"LAA-950pixel^3":[0.0],"LungVol pixel^3":[0.0],"LungVol voxs":[0.0],"PD15":[0.0],"StudyID":[NaN],"sex":[NaN],"vox volume pixel^3":[1.0]}  |
+----------------------+------------------------+------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--+
3 rows selected (17.768 seconds)

A trial which incorporates Image Segmentation also results in zero/null results:

select patientname,seriesDescription,studydate,runmap(run2(fetch_dicom_imagej(studyInstanceUID,seriesInstanceUID),"Segment Lung Tissue",""),"PD LAA Quantify SegmentedLung","") from stolz3pacs where success=true;

PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.54504.30000008112007153707800007751 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20081120.125332.60 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs6194165006507264746.properties --directory emptyDir
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.49001.30000008123113283818700000454 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20081231.103551.64 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs7131212569564495806.properties --directory emptyDir
PACSToolCall:-L SERIES -c osirix@localhost:11112 -b yeti -m SeriesInstanceUID=1.3.12.2.1107.5.1.4.50021.30000008051505383531200008814 -m StudyInstanceUID=1.2.276.0.18.14.200.2.0.0.20080515.113315.4 --store-tcs /var/folders/cj/p00m_p1137l5wpxrjr5wr62c0000gp/T/store_tcs7668734660244417243.properties --directory emptyDir
+----------------------+------------------------+------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--+
|     patientname      |   seriesDescription    | studydate  |                                                                                                                                    _c3                                                                                                                                    |
+----------------------+------------------------+------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--+
| Anonymous Sid 10007  | HWS+Thx art. 3.0 B30f  | 20081231   | {"FOV voxels ":[8.2313216E7],"LAA-1024%":[0.0],"LAA-1024pixel^3":[0.0],"LAA-900%":[0.0],"LAA-900pixel^3":[0.0],"LAA-950%":[0.0],"LAA-950pixel^3":[0.0],"LungVol pixel^3":[0.0],"LungVol voxs":[0.0],"PD15":[0.0],"StudyID":[NaN],"sex":[NaN],"vox volume pixel^3":[1.0]}  |
| Anonymous Sid 10201  | Thorax nativ 3.0 B30f  | 20081120   | {"FOV voxels ":[4.6923776E7],"LAA-1024%":[0.0],"LAA-1024pixel^3":[0.0],"LAA-900%":[0.0],"LAA-900pixel^3":[0.0],"LAA-950%":[0.0],"LAA-950pixel^3":[0.0],"LungVol pixel^3":[0.0],"LungVol voxs":[0.0],"PD15":[0.0],"StudyID":[NaN],"sex":[NaN],"vox volume pixel^3":[1.0]}  |
| Anonymous Sid 10113  | LE 3.0 B30f            | 20080515   | {"FOV voxels ":[5.7933824E7],"LAA-1024%":[0.0],"LAA-1024pixel^3":[0.0],"LAA-900%":[0.0],"LAA-900pixel^3":[0.0],"LAA-950%":[0.0],"LAA-950pixel^3":[0.0],"LungVol pixel^3":[0.0],"LungVol voxs":[0.0],"PD15":[0.0],"StudyID":[NaN],"sex":[NaN],"vox volume pixel^3":[1.0]}  |
+----------------------+------------------------+------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--+

Note: All values are Null.