Andrey Fedorov fedorov
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fedorov
/ Slicer3-BRAINSFitIGT-Case377.log
Created
March 23, 2016 15:30
See https://github.com/SlicerProstate/SliceTracker/wiki/Problematic-registration-cases
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| Type: Information | |
| Time: Tue Mar 22 17:00:11 2016 | |
| Description: BRAINSFitIGT completed without errors | |
| Type: Information | |
| Time: Tue Mar 22 17:00:10 2016 | |
| Description: BRAINSFitIGT standard output: | |
| TranformTypes: Rigid(1 of 2). |
fedorov
/ Slicer4-BRAINSFit-Case377-Andrey.log
Created
March 23, 2016 15:32
See https://github.com/SlicerProstate/SliceTracker/wiki/Problematic-registration-cases
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| General Registration (BRAINS) standard output: | |
| Original Fixed image origin[-71.857, -97.5889, 15.724, 0] | |
| TranformTypes: Rigid(1 of 3). | |
| TranformTypes: Affine(2 of 3). | |
| TranformTypes: BSpline(3 of 3). | |
| Initializing transform with useCenterOfROIAlign |
fedorov
/ Slicer4-BRAINSFit-Case377-Christian.log
Created
March 23, 2016 15:33
See https://github.com/SlicerProstate/SliceTracker/wiki/Problematic-registration-cases
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| General Registration (BRAINS) standard output: | |
| Original Fixed image origin[-71.857, -97.5889, 15.724, 0] | |
| TranformTypes: Rigid(1 of 1). | |
| Initializing transform with useCenterOfROIAlign | |
| Initializing transform with useCenterOfROIAlign to | |
| VersorRigid3DTransform (0x104ab77c0) | |
| RTTI typeinfo: itk::VersorRigid3DTransform<double> | |
| Reference Count: 2 |
fedorov
/ dcmqi-seg.jsonld
Created
May 6, 2016 20:32
Experiment to use JSON-LD for communicating metadata to dcmqi conversion tools http://github.com/qiicr/dcmqi
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| { | |
| "@context": { | |
| "ClinicalTrialSeriesID" : "http://dicom.nema.org/medical/dicom/current/output/chtml/part06/chapter_6.html#para_87c4e314-1f60-49f3-a379-5f6926316ec0", | |
| "ContentCreatorName" : "http://dicom.nema.org/medical/dicom/current/output/chtml/part06/chapter_6.html#para_1d93f33c-3935-49db-97c0-2dcad981f4aa", | |
| "ReaderID" : "ContentCreatorName", | |
| "SessionID" : "ClinicalTrialSeriesID", | |
| "ClinicalTrialTimePointID" : "http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.2.3.html#para_4d2ee376-92b4-4f23-9560-4fd0f5af77ad", | |
| "TimePoint" : "ClinicalTrialTimePointID", | |
| "SeriesDescription" : "http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.3.html#para_5fe2ee7d-82fc-44e4-893b-eecb8eb89550", | |
| "SeriesNumber" : "http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.8.8.html#para_cf392e6c-ab22-41a7-90ce-cf16145dc849", |
fedorov
/ adcdcmChecks.py
Created
August 17, 2016 18:28
Python script to complete DICOM checks using dciodvfy. To use, install pydicom dependency and run from the directory containing "ADC DICOM challenge" data (from Dariya).
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| import dicom, sys, os, subprocess, re | |
| typesMap = {} | |
| for sd, d, fs in os.walk("."): | |
| for f in fs: | |
| fpath = os.path.join(sd,f) | |
| try: | |
| dcm = dicom.read_file(fpath) | |
| location = fpath.split('/')[1] |
fedorov
/ aperio-delete-label.py
Created
October 1, 2016 02:40
— forked from malaterre/aperio-delete-label.py
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| #!/usr/bin/python | |
| # | |
| # Delete the label image from an Aperio SVS file. | |
| # | |
| # Copyright (c) 2012-2013 Carnegie Mellon University | |
| # All rights reserved. | |
| # | |
| # This program is free software: you can redistribute it and/or modify | |
| # it under the terms of the GNU Lesser General Public License as | |
| # published by the Free Software Foundation, version 2.1. |
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 |
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
/ 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
/ 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 */ |