Andrey Fedorov fedorov
🇺🇦
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
/ 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
/ 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
/ 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
/ 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
/ 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
/ gist:4f69f0f19da3c2ff0db1
Created
October 21, 2015 01:51
urlopen CERTIFICATE_VERIFY_FAILED error
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| import TCIABrowserLib | |
| c=TCIABrowserLib.TCIAClient(baseUrl='https://services.cancerimagingarchive.net/services/TCIA/TCIA/query') | |
| c.get_collection_values() |
fedorov
/ Config file passed to fCal and Slicer
Created
June 16, 2015 13:47
BWH - debugging Plus low FPS for prostate data acquisition
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| <PlusConfiguration version="2.3" PlusRevision="Plus-2.1.0.3427"> | |
| <DataCollection StartupDelaySec="1"> | |
| <DeviceSet Name="BK8818E depth 5.3cm w Slicer post calibration Q" Description="Epiphan frame grabber with Ascension EM trackers. Sensors in order: Red (111), Green (222), Blue (unmarked)."/> | |
| <Device | |
| Id="TrackerDevice" | |
| Type="Ascension3DG" | |
| AcquisitionRate="50" | |
| LocalTimeOffsetSec="0.15" | |
| FilterAcWideNotch="1" | |
| FilterAcNarrowNotch="0" |
fedorov
/ gist:67ac50a226b56ed12ae7
Created
June 16, 2015 13:36
Plus capture config file - debug low FPS
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| <PlusConfiguration version="2.3" PlusRevision="Plus-2.2.0.4177 - Win32"> | |
| <DataCollection StartupDelaySec="1"> | |
| <DeviceSet Name="BK8818E depth 5.3cm w Slicer post calibration Q" Description="Epiphan frame grabber with Ascension EM trackers. Sensors in order: Red (111), Green (222), Blue (unmarked)." /> | |
| <Device | |
| Id="TrackerDevice" | |
| Type="Ascension3DG" | |
| AcquisitionRate="50" | |
| LocalTimeOffsetSec="0.15" | |
| FilterAcWideNotch="1" | |
| FilterAcNarrowNotch="0" |
fedorov
/ gist:ef8ac0dcd787e3555b80
Created
June 16, 2015 13:35
Plus capture header file recorded from Slicer PlusRemote
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| ObjectType = Image | |
| NDims = 3 | |
| AnatomicalOrientation = RAI | |
| BinaryData = True | |
| BinaryDataByteOrderMSB = False | |
| CenterOfRotation = 0 0 0 | |
| CompressedData = False | |
| DimSize = 1280 1024 244 | |
| ElementNumberOfChannels = 1 | |
| ElementSpacing = 1 1 1 |