Get NIFTI Headers using itk-wasm and vtk.js

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1

Hi there,

Is it at all possible to access the full headers after reading a .nii file using itk-wasm and getting the vtkImageData? I see that we have some limited options available (e.g. getDirection, getOrigin), but what about the rest of the headers? In particular, I am looking for cal_min and cal_max to be able to dynamically set the color range of the image. Also would appreciate insights on how to do that regardless of whether it involves the headers!

Thanks!

2

itk-wasm currently doesn’t expose this extra metadata through vtkImageData. It would be interesting to see if itk-wasm itself can have facilities to return extra image metadata, maybe as a key/value map. @thewtex

3

Thanks for the response. We ended up writing a helper function that parses the ArrayBuffer directly. I’ll put that here in case it helps someone else in the future:

const struct = require('@aksel/structjs');

static parseHeader(buffer) {
    const niftiSpec = struct('<i35xB8h3f4h11fh2B4f8x104c2h18f20c4B');

    const nullTerm = (s) => {
      for (let i = 0; i < s.length; i += 1) {
        if (s[i] === '\0') {
          return s.slice(0, i).join('');
        }
      }
      return s.join('');
    };
    const v = niftiSpec.unpack(buffer);

    return {
      sizeof_hdr: v[0],
      dim_info: v[1],
      dim: v.slice(2, 10),
      intent_p1: v[10],
      intent_p2: v[11],
      intent_p3: v[12],
      intent_code: v[13],
      datatype: v[14],
      bitpix: v[15],
      slice_start: v[16],
      pixdim: v.slice(17, 25),
      vox_offset: v[25],
      scl_slope: v[26],
      scl_inter: v[27],
      slice_end: v[28],
      slice_code: v[29],
      xyzt_units: v[30],
      cal_max: v[31],
      cal_min: v[32],
      slice_duration: v[33],
      toffset: v[34],
      descrip: nullTerm(v.slice(35, 115)),
      aux_file: nullTerm(v.slice(115, 139)),
      qform_code: v[139],
      sform_code: v[140],
      quatern: v.slice(141, 144),
      quatern_offset: v.slice(144, 147),
      srow_x: v.slice(147, 151),
      srow_y: v.slice(151, 155),
      srow_z: v.slice(155, 159),
      intent_name: nullTerm(v.slice(159, 175)),
      magic: nullTerm(v.slice(175, 179)),
      ext: v.slice(179, 183),
    };
  }

 const arr = new Uint8Array([
      92, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 16, 0, 16, 0, 1, 0,
      1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 16, 0,
      32, 0, 0, 0, 0, 0, 128, 63, 0, 0, 92, 65, 0, 0, 92, 65, 0, 0, 160, 64, 0,
      0, 128, 63, 0, 0, 128, 63, 0, 0, 128, 63, 0, 0, 128, 63, 0, 0, 176, 67, 0,
      0, 128, 63, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 193, 0, 0, 0, 193, 0, 0, 0, 0, 0, 0, 92, 65, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 193, 0, 0, 0, 0, 0, 0, 92, 65, 0, 0, 0, 0,
      0, 0, 0, 193, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 160, 64, 0, 0, 0, 0, 0, 0, 0,
      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 110, 43, 49, 0, 0, 0, 0, 0,
    ]);
const buf = arr.buffer;

const headers = {
      sizeof_hdr: 348,
      dim_info: 0,
      dim: [2, 16, 16, 1, 1, 1, 1, 1],
      intent_p1: 0,
      intent_p2: 0,
      intent_p3: 0,
      intent_code: 0,
      datatype: 16,
      bitpix: 32,
      slice_start: 0,
      pixdim: [1, 13.75, 13.75, 5, 1, 1, 1, 1],
      vox_offset: 352,
      scl_slope: 1,
      scl_inter: 0,
      slice_end: 0,
      slice_code: 0,
      xyzt_units: 0,
      cal_max: 0,
      cal_min: 0,
      slice_duration: 0,
      toffset: 0,
      descrip: '',
      aux_file: '',
      qform_code: 0,
      sform_code: 2,
      quatern: [0, 0, 0],
      quatern_offset: [-8, -8, 0],
      srow_x: [13.75, 0, 0, -8],
      srow_y: [0, 13.75, 0, -8],
      srow_z: [0, 0, 5, 0],
      intent_name: '',
      magic: 'n+1',
      ext: [0, 0, 0, 0],
};

expect(NiftiUtils.parseHeader(buf)).to.deep.equal(headers);
1 Like