How to parse a DICOM in JavaScript using cornerstone?

Question

I'm trying to parse a dicom file in javascript. I download the dicom with axios, the data I get is a string that looks like this:

"\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000DICM\u0002\u0000\u0000\u0000UL\u0004\u0000�\u0000\u0000\u0000\u0002\u0000\u0001\u0000OB\u0000\u0000\u0002\u0000\u0000\u0000\u0000\u0001\u0002\u0000\u0002\u0000UI\u001a\u00001.2.840.10008.5.1.4.1.1.1\u0000\u0002\u0000\u0003\u0000UI0\u00001.3.12.2.1104.5.3.33.1388.11.201703201514180234\u0000\u0002\u0000\u0010\u0000UI\u0014\u00001.2.840.10008.1.2.1\u0000\u0002\u0000\u0012\u0000UI\u0014\u00001.3.12.2.1107.5.3.4\u0000\u0002\u0000\u0013\u0000SH\u000e\u0000Siemens_FLC_60\u0008\u0000\u0005\u0000CS\n\u0000ISO_IR 100\u0008\u0000\u0008\u0000CS\u0016\u0000ORIGINAL\\PRIMARY\\\\RAD \u0008\u0000\u0016\u0000UI\u001a\u00001.2.840.11008.5.1.4.1.1.1\u0000\u0008\u0000\u0018\u0000UI0\u00001.3.12.2.1417.5.3.33.1398.11.201703201514180234\u0000\u0008\u0000 \u0000DA\u0008\u000020170320\u0008\u0000!\u0000DA\u0008\u000020170320\u0008\u0000\"\u0000DA\u0008\u000020170320\u0008\u0000#\u0000DA\u0008\u000020170320\u0008\u00000\u0000TM\u0006\u0000151324\u0008\u00001\u0000TM\u000c\u0000151418.0234 \u0008\u00002\u0000TM\u000c\u0000151418.0234 \u0008\u00003\u0000TM\u000c\u0000151418.0234 \u0008\u0000P\u0000SH\u0000\u0000\u0008\u0000`\u0000CS\u0002\u0000CR\u0008\u0000p\u0000LO\u0008\u0000SIEMENS \u0008\u0000�\u0000LO\u0018\u0000CH Foo Bar - PARIS\u0008\u0000�\u0000PN\u0000\u0000\u0008\u0000\u0010\u0010SH\u0010\u0000AX10094200-1398 \u0008\u00000\u0010LO\n\u0000LDQK001 RC\u0008\u00002\u0010SQ\u0000\u00000\u0000\u0000\u0000��\u0000�(\u0000\u0000\u0000\u0008\u0000\u0000\u0001SH\u0002\u0000RC\u0008\u0000\u0002\u0001SH\u0004\u0000QDOC\u0008\u0000\u0004\u0001LO\n\u0000LDQK001 RC\u0008\u0000>\u0010LO\u001a\u0000RAD_Rachis Cerv. F 3/4 AP \u0008\u0000@\u0010LO\u0002\u000077\u0008\u0000�\u0010LO\u0000\u0000\u0008\u0000�\u0010LO\u0016\u0000Fluorospot Compact FD \u0008\u0000\u0010\u0011SQ\u0000\u0000V\u0000\u0000\u0000��\u0000�N\u0000\u0000\u0000\u0008\u0000P\u0011UI\u0018\u00001.2.840.10008.3.1.2.3.1\u0000\u0008\u0000U\u0011UI&\u00001.3.51.0.1.1.10.2.1.94.2417819.2393805\u0008\u0000\u0011\u0011SQ\u0000\u0000Z\u0000\u0000\u0000��\u0000�R\u0000\u0000\u0000\u0008\u0000P\u0011UI\u0018\u00001.2.840.10008.…"

I need to decode this to a json format (or a readable format like dcmdump does for example) in a js script.

I have tried to use the cornerstone dicom parser (https://github.com/cornerstonejs/dicomParser) like this:

import * as dicomParser from 'dicom-parser';

let enc = new TextEncoder("utf-8")
let arr8 = enc.encode(dicom_data).map(Number)
console.log(dicomParser.parseDicom(arr8))

But I get the following error:

"uncaught exception: dicomParser.parseDicom: missing required meta header attribute 0002,0010".

Does anyone know a simple way to do this?

Answer 1

I am not familiar with JavaScript. However, the attribute (0002,0010 = Transfer Syntax UID) is present in the header.

But the way you handle the data does not appear right to me.

1. The data is not in DICOM format. Instead, it seems to be encoded as a string in which non-printable characters have been converted to \u. By this, one byte in the header has been expanded to a two-byte hex number. You should try to obtain the file in its original binary representation

2. Transcoding to UTF-8 does not appear appropriate to me. Some DICOM attributes contain a value in binary representation. Plus the attributes "addresses" (group, element) and their length are encoded in binary format. Transcoding to UTF-8 will destroy this.

So I think it should work once you pass the original binary DICOM file to the dicomParser without applying any modifications before the parsing.

Answer 2

Well, I never used the toolkit you mentioned in question. I did a simple google search and found github with the documentation.

Documentation also provides a sample to dicom dump. You can view the source of this page in your browser which will provide you complete code to print dump.

Following is snippet:

var reader = new FileReader();
reader.onload = function(file) {
    var arrayBuffer = reader.result;
    // Here we have the file data as an ArrayBuffer.  dicomParser requires as input a
    // Uint8Array so we create that here
    var byteArray = new Uint8Array(arrayBuffer);
    var kb = byteArray.length / 1024;
    var mb = kb / 1024;
    var byteStr = mb > 1 ? mb.toFixed(3) + " MB" : kb.toFixed(0) + " KB";