Andrey Fedorov fedorov
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fedorov
/ tcga_nlst_sm_size.sql
Last active
April 6, 2022 03:43
Total size of TCGA and NLST DICOM SM data in IDC v8 release
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| WITH | |
| all_new_sm AS ( | |
| SELECT | |
| collection_id, | |
| COUNT(DISTINCT(SeriesInstanceUID)) AS num_series, | |
| ROUND(SUM(instance_size)/(1024*1024*1024),2) AS size_GB | |
| FROM | |
| `bigquery-public-data.idc_v8.dicom_all` | |
| WHERE | |
| (collection_id LIKE "tcga%" |
fedorov
/ google.js
Last active
June 2, 2022 14:25
This the template OHIF Viewer configuration file for connecting with Google Healthcare DICOM. See tutorial here: https://tinyurl.com/idc-ohif-gcp
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| window.config = { | |
| routerBasename: '/', | |
| enableGoogleCloudAdapter: true, | |
| // enable series filter parameter | |
| filterQueryParam: true, | |
| healthcareApiEndpoint: 'https://healthcare.googleapis.com/v1', | |
| servers: { | |
| // This is an array, but we'll only use the first entry for now | |
| dicomWeb: [], | |
| }, |
fedorov
/ firebase.json
Created
November 15, 2021 22:44
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| { | |
| "hosting": { | |
| "public": "public", | |
| "headers": [ | |
| { | |
| "source": "/**", | |
| "headers": [ | |
| { | |
| "key": "Cache-Control", | |
| "value": "no-cache, no-store, must-revalidate" |
fedorov
/ stack_trace.txt
Created
June 28, 2019 18:27
Slicer Jun 27 2019 crash after installing SimpleITK with pip
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| Process: Slicer [78341] | |
| Path: /Applications/Slicer.app/Contents/MacOS/Slicer | |
| Identifier: ??? | |
| Version: ??? (4.11.0-2019-06-27) | |
| Code Type: X86-64 (Native) | |
| Parent Process: zsh [738] | |
| Responsible: Slicer [78341] | |
| User ID: 501 | |
| Date/Time: 2019-06-28 14:19:39.643 -0400 |
fedorov
/ crash_trace.txt
Created
September 6, 2018 15:59
Slicer crash on invoking "Extension Manager", macOS, Sept 6, 2018, nightly
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| Process: Slicer [48459] | |
| Path: /Applications/Slicer.app/Contents/MacOS/Slicer | |
| Identifier: ??? | |
| Version: ??? (4.9.0-2018-09-04) | |
| Code Type: X86-64 (Native) | |
| Parent Process: ??? [1] | |
| Responsible: Slicer [48459] | |
| User ID: 501 | |
| Date/Time: 2018-09-06 11:58:11.619 -0400 |
fedorov
/ A.repeatability.7.19.16.R
Created
September 29, 2017 21:16
Repeatability analysis R script
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| rm(list=ls()) | |
| library(ICC) | |
| dat<-read.table('data20160211.csv',header=TRUE,sep=';') | |
| library(outliers); library(lme4); library(lmerTest); library(boot) | |
| library(multcomp) | |
| types<-c("ADC1400", "SUB", "T2AX") | |
| structures<-c("PeripheralZone", "TumorROI_PZ_1", "NormalROI_PZ_1", | |
| "WholeGland") | |
| get.dat<-function(quantity, structures, types, dat){ | |
| X<-dat[dat$Quantity==quantity & !is.na(dat$Value) & |
fedorov
/ read1500.cc
Created
August 12, 2017 19:58
Sample program reading an SR document based on TID 1500 and printing details on the measurements
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| /* | |
| * Sample program reading an SR document based on TID 1500 and printing details on the measurements | |
| * | |
| * Author: J. Riesmeier, Oldenburg, Germany | |
| * | |
| */ | |
| #include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */ |
fedorov
/ ITK header - TCGA-02-0006_1996.08.23_GlistrBoost.nii.gz
Last active
August 4, 2017 16:42
nibabel difference between TCIA-GBM segmentation headers
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| LargestPossibleRegion: | |
| Dimension: 3 | |
| Index: [0, 0, 0] | |
| Size: [240, 240, 155] | |
| BufferedRegion: | |
| Dimension: 3 | |
| Index: [0, 0, 0] | |
| Size: [240, 240, 155] | |
| RequestedRegion: | |
| Dimension: 3 |
fedorov
/ metadata.json
Created
April 26, 2017 21:32
dcmqi metadata JSON for the FreeSurfer brain label conversion use case
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| { | |
| "ContentCreatorName": "FreeSurfer", | |
| "ClinicalTrialSeriesID": "Session1", | |
| "ClinicalTrialTimePointID": "1", | |
| "SeriesDescription": "Segmentation", | |
| "SeriesNumber": "300", | |
| "InstanceNumber": "1", | |
| "BodyPartExamined": "BRAIN", | |
| "segmentAttributes": [ | |
| [ |
fedorov
/ Linker command line after upgrade
Last active
February 23, 2017 18:20
Slicer extension build problems after upgrade of ITK to 4.11
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| /usr/bin/c++ -Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings -D_FORTIFY_SOURCE=2 -fdiagnostics-show-option -Wl,--no-undefined -fstack-protector-all -Wno-deprecated -Woverloaded-virtual -Wstrict-null-sentinel -msse2 -Wall -Wno-deprecated -msse2 -g -lpthread CMakeFiles/paramap2itkimage.dir/home/fedorov/builds/Slicer4-Debug/Slicer-build/Base/CLI/SEMCommandLineLibraryWrapper.cxx.o -o ../../lib/Slicer-4.7/cli-modules/paramap2itkimage -L/home/fedorov/builds/Slicer4-Debug/teem-build/bin -Wl,-rpath,/home/fedorov/builds/Slicer4-Debug/teem-build/bin:/home/fedorov/builds/Slicer4-Debug/Slicer-build/bin:/home/fedorov/builds/Slicer4-Debug/JsonCpp-build/src/lib_json/.:/home/fedorov/builds/Slicer4-Debug/DCMTK-build/lib: ../../lib/Slicer-4.7/cli-modules/libparamap2itkimageLib.a /home/fedorov/builds/Slicer4-Debug/Slicer-build/bin/libITKFactoryRegistration.so /home/fedorov/builds/Slicer4-Debug/JsonCpp-build/src/lib_json/./libjsoncpp.so ../../bin/libdcmqi.a /home/fedorov/builds/Slicer4-De |