Here is the output of that command you suggested: ❯ showinf -nopix /Users/ilangold/Documents/medical_images/DICOM/ST000001/SE000001/CT000055ĭicomReader initializing /Users/ilangold/Documents/medical_images/DICOM/ST000001/SE000001/CT000055įilename = /Users/ilangold/Documents/medical_images/DICOM/ST000001/SE000001/CT000055 Ah, ok there is a DICOMDIR file in addition to the actual directory that maybe I should point to? I get a :1:75: Character reference " " is an invalid XML character.Įxception in thread "main" : lineNumber: 1 columnNumber: 75 Character reference " " is an invalid XML character.Īt .asXMLElement(XMLAnnotation.java:263)Īt .asXMLElement(StructuredAnnotations.java:681)Īt .asXMLElement(OME.java:931)Īt .asXMLElement(OME.java:771)Īt .dumpXML(AbstractOMEXMLMetadata.java:110)Īt .dumpXML(OMEXMLMetadataImpl.java:105)Īt .dumpXML(OMEPyramidStore.java:81)Īt .getOMEXML(OMEXMLServiceImpl.java:471)Īt .testConvert(ImageConverter.java:544)Īt .main(ImageConverter.java:1095)Ĭaused by: lineNumber: 1 columnNumber: 75 Character reference " " is an invalid XML character.Īt .DOMParser.parse(Unknown Source)Īt .DocumentBuilderImpl.parse(Unknown Source)Īt .asXMLElement(XMLAnnotation.java:259)Īpologies, Josh, I was using bioformats2raw to try to convert via bioformats2raw /Users/ilangold/Documents/medical_images/DICOMDIR /Users/ilangold/Documents/medical_images/DI COMDIR.dir to get that bad character error.
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