@niivue/niivue 0.22.2 → 0.23.0

package/src/nvimage.js

@@ -1,11 +1,20 @@
-import * as nifti from "nifti-reader-js";
+import nifti from "nifti-reader-js";
+import daikon from "daikon";
 import { v4 as uuidv4 } from "uuid";
-import * as mat from "gl-matrix";
+import { mat3, mat4, vec3, vec4 } from "gl-matrix";
 import * as cmaps from "./cmaps";
+import * as fflate from "fflate";
 import { NiivueObject3D } from "./niivue-object3D";
 import { Log } from "./logger";
 const log = new Log();
 
+function isPlatformLittleEndian() {
+  //inspired by https://github.com/rii-mango/Papaya
+  var buffer = new ArrayBuffer(2);
+  new DataView(buffer).setInt16(0, 256, true);
+  return new Int16Array(buffer)[0] === 256;
+}
+
 /**
  * query all available color maps that can be applied to volumes
  * @param {boolean} [sort=true] whether or not to sort the returned array
@@ -17,6 +26,7 @@ const log = new Log();
 
 /**
  * @class NVImage
+ * @type NVImage
  * @description
  * a NVImage encapsulates some images data and provides methods to query and operate on images
  * @constructor
@@ -29,15 +39,17 @@ const log = new Log();
  * @param {boolean} [ignoreZeroVoxels=false] whether or not to ignore zero voxels in setting the robust range of display values
  * @param {boolean} [visible=true] whether or not this image is to be visible
  */
-export var NVImage = function (
-  dataBuffer,
+export function NVImage(
+  dataBuffer, // can be an array of Typed arrays or just a typed array. If an array of Typed arrays then it is assumed you are loading DICOM (perhaps the only real use case?)
   name = "",
   colorMap = "gray",
   opacity = 1.0,
+  pairedImgData = null,
   trustCalMinMax = true,
   percentileFrac = 0.02,
   ignoreZeroVoxels = false,
   visible = true,
+  isDICOMDIR = false,
   useQFormNotSForm = false
 ) {
   // https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
@@ -65,18 +77,103 @@ export var NVImage = function (
   this.name = name;
   this.id = uuidv4();
   this.colorMap = colorMap;
+  this.frame4D = 0; //indexed from 0!
   this.opacity = opacity > 1.0 ? 1.0 : opacity; //make sure opacity can't be initialized greater than 1 see: #107 and #117 on github
   this.percentileFrac = percentileFrac;
   this.ignoreZeroVoxels = ignoreZeroVoxels;
   this.trustCalMinMax = trustCalMinMax;
   this.visible = visible;
+  this.series = []; // for concatenating dicom images
 
   // Added to support zerosLike
   if (!dataBuffer) {
     return;
   }
+  var re = /(?:\.([^.]+))?$/;
+  let ext = re.exec(name)[1] || "";
+  ext = ext.toUpperCase();
+  if (ext === "GZ") {
+    ext = re.exec(name.slice(0, -3))[1]; //img.trk.gz -> img.trk
+    ext = ext.toUpperCase();
+  }
+  let imgRaw = null;
+  this.hdr = null;
+  if (ext === "" && isDICOMDIR && Array.isArray(dataBuffer)) {
+    imgRaw = this.readDICOM(dataBuffer);
+  } else if (ext === "MIH" || ext === "MIF") {
+    imgRaw = this.readMIF(dataBuffer, pairedImgData); //detached
+  } else if (ext === "NHDR" || ext === "NRRD") {
+    imgRaw = this.readNRRD(dataBuffer, pairedImgData); //detached
+  } else if (ext === "MHD" || ext === "MHA") {
+    imgRaw = this.readMHA(dataBuffer); //to do: pairedImgData
+  } else if (ext === "MGH" || ext === "MGZ") {
+    imgRaw = this.readMGH(dataBuffer);
+  } else if (ext === "V") {
+    imgRaw = this.readECAT(dataBuffer);
+  } else if (ext === "V16") {
+    imgRaw = this.readV16(dataBuffer);
+  } else if (ext === "VMR") {
+    imgRaw = this.readVMR(dataBuffer);
+  } else if (ext === "HEAD") {
+    imgRaw = this.readHEAD(dataBuffer, pairedImgData); //paired = .BRIK
+  } else if (ext === "NII") {
+    this.hdr = nifti.readHeader(dataBuffer);
+    if (this.hdr.cal_min === 0 && this.hdr.cal_max === 255)
+      this.hdr.cal_max = 0.0;
+    if (nifti.isCompressed(dataBuffer)) {
+      imgRaw = nifti.readImage(this.hdr, nifti.decompress(dataBuffer));
+    } else {
+      imgRaw = nifti.readImage(this.hdr, dataBuffer);
+    }
+  } else {
+    //DICOMs do not always end .dcm, so DICOM is our format of last resort
+    imgRaw = this.readDICOM(dataBuffer);
+    // if loading a DICOM directory
+  }
+  this.nFrame4D = 1;
+  for (let i = 4; i < 7; i++)
+    if (this.hdr.dims[i] > 1) this.nFrame4D *= this.hdr.dims[i];
+  this.nVox3D = this.hdr.dims[1] * this.hdr.dims[2] * this.hdr.dims[3];
+  let nVol4D = imgRaw.byteLength / this.nVox3D / (this.hdr.numBitsPerVoxel / 8);
+  if (nVol4D !== this.nFrame4D)
+    console.log(
+      "This header does not match voxel data",
+      this.hdr,
+      imgRaw.byteLength
+    );
+  if (
+    this.hdr.intent_code === 1007 &&
+    this.nFrame4D === 3 &&
+    this.hdr.datatypeCode === this.DT_FLOAT
+  ) {
+    let tmp = new Float32Array(imgRaw);
+    let f32 = tmp.slice();
+    this.hdr.datatypeCode = this.DT_RGB;
+    this.nFrame4D = 1;
+    for (let i = 4; i < 7; i++) this.hdr.dims[i] = 1;
+    this.hdr.dims[0] = 3; //3D
+    imgRaw = new Uint8Array(this.nVox3D * 3); //*3 for RGB
+    let mx = Math.abs(f32[0]);
+    for (let i = 0; i < this.nVox3D * 3; i++)
+      mx = Math.max(mx, Math.abs(f32[i]));
+    let slope = 1.0;
+    if (mx > 0) slope = 1.0 / mx;
 
-  this.hdr = nifti.readHeader(dataBuffer);
+    let nVox3D2 = this.nVox3D * 2;
+    let j = 0;
+    for (let i = 0; i < this.nVox3D; i++) {
+      imgRaw[j] = 255.0 * Math.abs(f32[i] * slope);
+      imgRaw[j + 1] = 255.0 * Math.abs(f32[i + this.nVox3D] * slope);
+      imgRaw[j + 2] = 255.0 * Math.abs(f32[i + nVox3D2] * slope);
+      j += 3;
+    }
+  } //NIFTI_INTENT_VECTOR: this is a RGB tensor
+  if (
+    this.hdr.pixDims[1] === 0.0 ||
+    this.hdr.pixDims[2] === 0.0 ||
+    this.hdr.pixDims[3] === 0.0
+  )
+    console.log("pixDims not plausible", this.hdr);
   function isAffineOK(mtx) {
     //A good matrix should not have any components that are not a number
     //A good spatial transformation matrix should not have a row or column that is all zeros
@@ -175,19 +272,53 @@ export var NVImage = function (
     ];
     this.hdr.affine = affine;
   } //defective affine
-  let imgRaw = null;
-  if (nifti.isCompressed(dataBuffer)) {
-    imgRaw = nifti.readImage(this.hdr, nifti.decompress(dataBuffer));
-  } else {
-    imgRaw = nifti.readImage(this.hdr, dataBuffer);
-  }
-
+  //swap data if foreign endian:
+  if (
+    this.hdr.datatypeCode !== this.DT_RGB &&
+    this.hdr.datatypeCode !== this.DT_RGBA32 &&
+    this.hdr.littleEndian !== isPlatformLittleEndian() &&
+    this.hdr.numBitsPerVoxel > 8
+  ) {
+    if (this.hdr.numBitsPerVoxel === 16) {
+      //inspired by https://github.com/rii-mango/Papaya
+      var u16 = new Uint16Array(imgRaw);
+      for (let i = 0; i < u16.length; i++) {
+        let val = u16[i];
+        u16[i] = ((((val & 0xff) << 8) | ((val >> 8) & 0xff)) << 16) >> 16; // since JS uses 32-bit  when bit shifting
+      }
+    } else if (this.hdr.numBitsPerVoxel === 32) {
+      //inspired by https://github.com/rii-mango/Papaya
+      var u32 = new Uint32Array(imgRaw);
+      for (let i = 0; i < u32.length; i++) {
+        let val = u32[i];
+        u32[i] =
+          ((val & 0xff) << 24) |
+          ((val & 0xff00) << 8) |
+          ((val >> 8) & 0xff00) |
+          ((val >> 24) & 0xff);
+      }
+    } else if (this.hdr.numBitsPerVoxel === 64) {
+      //inspired by MIT licensed code: https://github.com/rochars/endianness
+      let numBytesPerVoxel = this.hdr.numBitsPerVoxel / 8;
+      var u8 = new Uint8Array(imgRaw);
+      for (let index = 0; index < u8.length; index += numBytesPerVoxel) {
+        let offset = bytesPer - 1;
+        for (let x = 0; x < offset; x++) {
+          let theByte = u8[index + x];
+          u8[index + x] = u8[index + offset];
+          u8[index + offset] = theByte;
+          offset--;
+        }
+      }
+    } //if 64-bits
+  } //swap byte order
   switch (this.hdr.datatypeCode) {
     case this.DT_UNSIGNED_CHAR:
       this.img = new Uint8Array(imgRaw);
       break;
     case this.DT_SIGNED_SHORT:
       this.img = new Int16Array(imgRaw);
+
       break;
     case this.DT_FLOAT:
       this.img = new Float32Array(imgRaw);
@@ -204,51 +335,55 @@ export var NVImage = function (
     case this.DT_RGBA32:
       this.img = new Uint8Array(imgRaw);
       break;
-    case this.DT_INT8:
+    case this.DT_INT8: {
       let i8 = new Int8Array(imgRaw);
       var vx8 = i8.length;
       this.img = new Int16Array(vx8);
-      for (var i = 0; i < vx8 - 1; i++) this.img[i] = i8[i];
+      for (let i = 0; i < vx8 - 1; i++) this.img[i] = i8[i];
       this.hdr.datatypeCode = this.DT_SIGNED_SHORT;
       break;
-    case this.DT_UINT32:
+    }
+    case this.DT_UINT32: {
       let u32 = new Uint32Array(imgRaw);
       var vx32 = u32.length;
       this.img = new Float64Array(vx32);
-      for (var i = 0; i < vx32 - 1; i++) this.img[i] = u32[i];
+      for (let i = 0; i < vx32 - 1; i++) this.img[i] = u32[i];
       this.hdr.datatypeCode = this.DT_DOUBLE;
       break;
-    case this.DT_SIGNED_INT:
+    }
+    case this.DT_SIGNED_INT: {
       let i32 = new Int32Array(imgRaw);
       var vxi32 = i32.length;
       this.img = new Float64Array(vxi32);
-      for (var i = 0; i < vxi32 - 1; i++) this.img[i] = i32[i];
+      for (let i = 0; i < vxi32 - 1; i++) this.img[i] = i32[i];
       this.hdr.datatypeCode = this.DT_DOUBLE;
       break;
-    case this.DT_INT64:
+    }
+    case this.DT_INT64: {
+      // eslint-disable-next-line no-undef
       let i64 = new BigInt64Array(imgRaw);
       let vx = i64.length;
       this.img = new Float64Array(vx);
-      for (var i = 0; i < vx - 1; i++) this.img[i] = Number(i64[i]);
+      for (let i = 0; i < vx - 1; i++) this.img[i] = Number(i64[i]);
       this.hdr.datatypeCode = this.DT_DOUBLE;
       break;
+    }
     default:
       throw "datatype " + this.hdr.datatypeCode + " not supported";
   }
-
   this.calculateRAS();
   this.calMinMax();
-};
+}
 
 NVImage.prototype.calculateOblique = function () {
   let LPI = this.vox2mm([0.0, 0.0, 0.0], this.matRAS);
   let X1mm = this.vox2mm([1.0 / this.pixDimsRAS[1], 0.0, 0.0], this.matRAS);
   let Y1mm = this.vox2mm([0.0, 1.0 / this.pixDimsRAS[2], 0.0], this.matRAS);
   let Z1mm = this.vox2mm([0.0, 0.0, 1.0 / this.pixDimsRAS[3]], this.matRAS);
-  mat.vec3.subtract(X1mm, X1mm, LPI);
-  mat.vec3.subtract(Y1mm, Y1mm, LPI);
-  mat.vec3.subtract(Z1mm, Z1mm, LPI);
-  let oblique = mat.mat4.fromValues(
+  vec3.subtract(X1mm, X1mm, LPI);
+  vec3.subtract(Y1mm, Y1mm, LPI);
+  vec3.subtract(Z1mm, Z1mm, LPI);
+  let oblique = mat4.fromValues(
     X1mm[0],
     X1mm[1],
     X1mm[2],
@@ -266,15 +401,1291 @@ NVImage.prototype.calculateOblique = function () {
     0,
     1
   );
-  this.obliqueRAS = mat.mat4.clone(oblique);
-  let XY = Math.abs(90 - mat.vec3.angle(X1mm, Y1mm) * (180 / Math.PI));
-  let XZ = Math.abs(90 - mat.vec3.angle(X1mm, Z1mm) * (180 / Math.PI));
-  let YZ = Math.abs(90 - mat.vec3.angle(Y1mm, Z1mm) * (180 / Math.PI));
+  this.obliqueRAS = mat4.clone(oblique);
+  let XY = Math.abs(90 - vec3.angle(X1mm, Y1mm) * (180 / Math.PI));
+  let XZ = Math.abs(90 - vec3.angle(X1mm, Z1mm) * (180 / Math.PI));
+  let YZ = Math.abs(90 - vec3.angle(Y1mm, Z1mm) * (180 / Math.PI));
   let maxShear = Math.max(Math.max(XY, XZ), YZ);
   if (maxShear > 0.1)
     log.debug("Warning: shear detected (gantry tilt) of %f degrees", maxShear);
 };
 
+NVImage.prototype.THD_daxes_to_NIFTI = function (
+  xyzDelta,
+  xyzOrigin,
+  orientSpecific
+) {
+  //https://github.com/afni/afni/blob/d6997e71f2b625ac1199460576d48f3136dac62c/src/thd_niftiwrite.c#L315
+  let hdr = this.hdr;
+  hdr.sform_code = 2;
+  const ORIENT_xyz = "xxyyzzg"; //note strings indexed from 0!
+  let nif_x_axnum = -1;
+  let nif_y_axnum = -1;
+  let nif_z_axnum = -1;
+  let axcode = ["x", "y", "z"];
+  axcode[0] = ORIENT_xyz[orientSpecific[0]];
+  axcode[1] = ORIENT_xyz[orientSpecific[1]];
+  axcode[2] = ORIENT_xyz[orientSpecific[2]];
+  let axstep = xyzDelta.slice(0, 3);
+  let axstart = xyzOrigin.slice(0, 3);
+  for (var ii = 0; ii < 3; ii++) {
+    if (axcode[ii] === "x") nif_x_axnum = ii;
+    else if (axcode[ii] === "y") nif_y_axnum = ii;
+    else nif_z_axnum = ii;
+  }
+  if (nif_x_axnum < 0 || nif_y_axnum < 0 || nif_z_axnum < 0) return; //not assigned
+  if (
+    nif_x_axnum === nif_y_axnum ||
+    nif_x_axnum === nif_z_axnum ||
+    nif_y_axnum === nif_z_axnum
+  )
+    return; //not assigned
+  hdr.pixDims[1] = Math.abs(axstep[0]);
+  hdr.pixDims[2] = Math.abs(axstep[1]);
+  hdr.pixDims[3] = Math.abs(axstep[2]);
+  hdr.affine = [
+    [1, 0, 0, 0],
+    [0, 1, 0, 0],
+    [0, 0, 1, 0],
+    [0, 0, 0, 1],
+  ];
+  hdr.affine[0][nif_x_axnum] = -axstep[nif_x_axnum];
+  hdr.affine[1][nif_y_axnum] = -axstep[nif_y_axnum];
+  hdr.affine[2][nif_z_axnum] = axstep[nif_z_axnum];
+  hdr.affine[0][3] = -axstart[nif_x_axnum];
+  hdr.affine[1][3] = -axstart[nif_y_axnum];
+  hdr.affine[2][3] = axstart[nif_z_axnum];
+};
+
+NVImage.prototype.SetPixDimFromSForm = function () {
+  let m = this.hdr.affine;
+  let mat = mat4.fromValues(
+    m[0][0],
+    m[0][1],
+    m[0][2],
+    m[0][3],
+    m[1][0],
+    m[1][1],
+    m[1][2],
+    m[1][3],
+    m[2][0],
+    m[2][1],
+    m[2][2],
+    m[2][3],
+    m[3][0],
+    m[3][1],
+    m[3][2],
+    m[3][3]
+  );
+  let mm000 = this.vox2mm([0, 0, 0], mat);
+  let mm100 = this.vox2mm([1, 0, 0], mat);
+  vec3.subtract(mm100, mm100, mm000);
+  let mm010 = this.vox2mm([0, 1, 0], mat);
+  vec3.subtract(mm010, mm010, mm000);
+  let mm001 = this.vox2mm([0, 0, 1], mat);
+  vec3.subtract(mm001, mm001, mm000);
+  this.hdr.pixDims[1] = vec3.length(mm100);
+  this.hdr.pixDims[2] = vec3.length(mm010);
+  this.hdr.pixDims[3] = vec3.length(mm001);
+};
+
+function getBestTransform(imageDirections, voxelDimensions, imagePosition) {
+  //https://github.com/rii-mango/Papaya/blob/782a19341af77a510d674c777b6da46afb8c65f1/src/js/volume/dicom/header-dicom.js#L605
+  /*Copyright (c) 2012-2015, RII-UTHSCSA
+All rights reserved.
+
+THIS PRODUCT IS NOT FOR CLINICAL USE.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
+following conditions are met:
+
+ - Redistributions of source code must retain the above copyright notice, this list of conditions and the following
+   disclaimer.
+
+ - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided with the distribution.
+
+ - Neither the name of the RII-UTHSCSA nor the names of its contributors may be used to endorse or promote products
+   derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+  var cosines = imageDirections,
+    m = null;
+  if (cosines) {
+    var vs = {
+      colSize: voxelDimensions[0],
+      rowSize: voxelDimensions[1],
+      sliceSize: voxelDimensions[2],
+    };
+    var coord = imagePosition;
+    var cosx = [cosines[0], cosines[1], cosines[2]];
+    var cosy = [cosines[3], cosines[4], cosines[5]];
+    var cosz = [
+      cosx[1] * cosy[2] - cosx[2] * cosy[1],
+      cosx[2] * cosy[0] - cosx[0] * cosy[2],
+      cosx[0] * cosy[1] - cosx[1] * cosy[0],
+    ];
+    m = [
+      [
+        cosx[0] * vs.colSize * -1,
+        cosy[0] * vs.rowSize * -1,
+        cosz[0] * vs.sliceSize * -1,
+        -1 * coord[0],
+      ],
+      [
+        cosx[1] * vs.colSize * -1,
+        cosy[1] * vs.rowSize * -1,
+        cosz[1] * vs.sliceSize * -1,
+        -1 * coord[1],
+      ],
+      [
+        cosx[2] * vs.colSize,
+        cosy[2] * vs.rowSize,
+        cosz[2] * vs.sliceSize,
+        coord[2],
+      ],
+      [0, 0, 0, 1],
+    ];
+  }
+  return m;
+} // getBestTransform()
+
+NVImage.prototype.readDICOM = function (buf) {
+  this.series = new daikon.Series();
+  // parse DICOM file
+  if (Array.isArray(buf)) {
+    for (let i = 0; i < buf.length; i++) {
+      let image = daikon.Series.parseImage(new DataView(buf[i]));
+      if (image === null) {
+        console.error(daikon.Series.parserError);
+      } else if (image.hasPixelData()) {
+        // if it's part of the same series, add it
+        if (
+          this.series.images.length === 0 ||
+          image.getSeriesId() === this.series.images[0].getSeriesId()
+        ) {
+          this.series.addImage(image);
+        }
+      } // if hasPixelData
+    } // for i
+  } else {
+    // Array.isArray
+    var image = daikon.Series.parseImage(new DataView(buf));
+    if (image === null) {
+      console.error(daikon.Series.parserError);
+    } else if (image.hasPixelData()) {
+      // if it's part of the same series, add it
+      if (
+        this.series.images.length === 0 ||
+        image.getSeriesId() === this.series.images[0].getSeriesId()
+      ) {
+        this.series.addImage(image);
+      }
+    }
+  }
+  // order the image files, determines number of frames, etc.
+  this.series.buildSeries();
+  // output some header info
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.scl_inter = 0;
+  hdr.scl_slope = 1;
+  if (this.series.images[0].getDataScaleIntercept())
+    hdr.scl_inter = this.series.images[0].getDataScaleIntercept();
+  if (this.series.images[0].getDataScaleSlope())
+    hdr.scl_slope = this.series.images[0].getDataScaleSlope();
+  if (hdr.scl_slope === 0) hdr.scl_slope;
+  hdr.dims = [3, 1, 1, 1, 0, 0, 0, 0];
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  hdr.dims[1] = this.series.images[0].getCols();
+  hdr.dims[2] = this.series.images[0].getRows();
+  hdr.dims[3] = this.series.images[0].getNumberOfFrames();
+  if (this.series.images.length > 1) {
+    if (hdr.dims[3] > 1)
+      console.log(
+        "To Do: multiple slices per file and multiple files (XA30 DWI)"
+      );
+    hdr.dims[3] = this.series.images.length;
+  }
+  let rc = this.series.images[0].getPixelSpacing(); //TODO: order?
+  hdr.pixDims[1] = rc[0];
+  hdr.pixDims[2] = rc[1];
+  hdr.pixDims[3] = Math.max(
+    this.series.images[0].getSliceGap(),
+    this.series.images[0].getSliceThickness()
+  );
+  hdr.pixDims[4] = this.series.images[0].getTR() / 1000.0; //msec -> sec
+  let dt = this.series.images[0].getDataType(); //2=int,3=uint,4=float,
+  let bpv = this.series.images[0].getBitsAllocated();
+  hdr.numBitsPerVoxel = bpv;
+  this.hdr.littleEndian = this.series.images[0].littleEndian;
+  if (bpv === 8 && dt === 2) hdr.datatypeCode = this.DT_INT8;
+  else if (bpv === 8 && dt === 3) hdr.datatypeCode = this.DT_UNSIGNED_CHAR;
+  else if (bpv === 16 && dt === 2) hdr.datatypeCode = this.DT_SIGNED_SHORT;
+  else if (bpv === 16 && dt === 3) hdr.datatypeCode = this.DT_UINT16;
+  else if (bpv === 32 && dt === 2) hdr.datatypeCode = this.DT_SIGNED_INT;
+  else if (bpv === 32 && dt === 3) hdr.datatypeCode = this.DT_UINT32;
+  else if (bpv === 32 && dt === 4) hdr.datatypeCode = this.DT_FLOAT;
+  else if (bpv === 64 && dt === 4) hdr.datatypeCode = this.DT_DOUBLE;
+  else console.log("Unsupported DICOM format: " + dt + " " + bpv);
+  let voxelDimensions = hdr.pixDims.slice(1, 4);
+  //console.log("dir", this.series.images[0].getImageDirections());
+  //console.log("pos", this.series.images[0].getImagePosition());
+  //console.log("dims", voxelDimensions);
+  let m = getBestTransform(
+    this.series.images[0].getImageDirections(),
+    voxelDimensions,
+    this.series.images[0].getImagePosition()
+  );
+  if (m) {
+    hdr.sform_code = 1;
+    hdr.affine = [
+      [m[0][0], m[0][1], m[0][2], m[0][3]],
+      [m[1][0], m[1][1], m[1][2], m[1][3]],
+      [m[2][0], m[2][1], m[2][2], m[2][3]],
+      [0, 0, 0, 1],
+    ];
+  }
+  console.log("DICOM", this.series.images[0]);
+  console.log("NIfTI", hdr);
+  let imgRaw = [];
+  //let byteLength = hdr.dims[1] * hdr.dims[2] * hdr.dims[3] * (bpv / 8);
+  let data;
+  let length = this.series.validatePixelDataLength(this.series.images[0]);
+  let buffer = new Uint8Array(
+    new ArrayBuffer(length * this.series.images.length)
+  );
+  // implementation copied from:
+  // https://github.com/rii-mango/Daikon/blob/bbe08bad9758dfbdf31ca22fb79048c7bad85706/src/series.js#L496
+  for (let i = 0; i < this.series.images.length; i++) {
+    if (this.series.isMosaic) {
+      data = this.series.getMosaicData(
+        this.series.images[i],
+        this.series.images[i].getPixelDataBytes()
+      );
+    } else {
+      data = this.series.images[i].getPixelDataBytes();
+    }
+    length = this.series.validatePixelDataLength(this.series.images[i]);
+    this.series.images[i].clearPixelData();
+    buffer.set(new Uint8Array(data, 0, length), length * i);
+  } // for images.length
+  imgRaw = buffer.buffer;
+  return imgRaw;
+}; // readDICOM()
+
+NVImage.prototype.readECAT = function (buffer) {
+  //https://github.com/openneuropet/PET2BIDS/tree/28aae3fab22309047d36d867c624cd629c921ca6/ecat_validation/ecat_info
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.dims = [3, 1, 1, 1, 0, 0, 0, 0];
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  var reader = new DataView(buffer);
+  var raw = buffer;
+  let signature = reader.getInt32(0, false); //"MATR"
+  let filetype = reader.getInt16(50, false);
+  if (signature !== 1296127058 || filetype < 1 || filetype > 14) {
+    console.log("Not a valid ECAT file");
+    return;
+  }
+  //list header, starts at 512 bytes: int32_t hdr[4], r[31][4];
+  let pos = 512; //512=main header, 4*32-bit hdr
+  let vols = 0;
+  let frame_duration = [];
+  let rawImg = [];
+  while (true) {
+    //read 512 block lists
+    let hdr0 = reader.getInt32(pos, false);
+    let hdr3 = reader.getInt32(pos + 12, false);
+    if (hdr0 + hdr3 !== 31) break;
+    let lpos = pos + 20; //skip hdr and read slice offset (r[0][1])
+    let r = 0;
+    let voloffset = 0;
+    while (r < 31) {
+      //r[0][1]...r[30][1]
+      voloffset = reader.getInt32(lpos, false);
+      lpos += 16; //e.g. r[0][1] to r[1][1]
+      if (voloffset === 0) break;
+      r++;
+      let ipos = voloffset * 512; //image start position
+      let spos = ipos - 512; //subheader for matrix image, immediately before image
+      let data_type = reader.getUint16(spos, false);
+      hdr.dims[1] = reader.getUint16(spos + 4, false);
+      hdr.dims[2] = reader.getUint16(spos + 6, false);
+      hdr.dims[3] = reader.getUint16(spos + 8, false);
+      let scale_factor = reader.getFloat32(spos + 26, false);
+      hdr.pixDims[1] = reader.getFloat32(spos + 34, false) * 10.0; //cm -> mm
+      hdr.pixDims[2] = reader.getFloat32(spos + 38, false) * 10.0; //cm -> mm
+      hdr.pixDims[3] = reader.getFloat32(spos + 42, false) * 10.0; //cm -> mm
+      hdr.pixDims[4] = reader.getUint32(spos + 46, false) / 1000.0; //ms -> sec
+      frame_duration.push(hdr.pixDims[4]);
+      let nvox3D = hdr.dims[1] * hdr.dims[2] * hdr.dims[3];
+      var newImg = new Float32Array(nvox3D); //convert to float32 as scale varies
+      if (data_type == 1)
+        //uint8
+        for (var i = 0; i < nvox3D; i++) {
+          newImg[i] = reader.getUint8(ipos) * scale_factor;
+          ipos++;
+        }
+      else if (data_type == 6) {
+        //uint16
+        for (var i = 0; i < nvox3D; i++) {
+          newImg[i] = reader.getUint16(ipos, false) * scale_factor;
+          ipos += 2;
+        }
+      } else if (ihdr.data_type == 7) {
+        //uint32
+        for (var i = 0; i < nvox3D; i++) {
+          newImg[i] = reader.getUint32(ipos, false) * scale_factor;
+          ipos += 4;
+        }
+      } else console.log("Unknown ECAT data type " + data_type);
+      let prevImg = rawImg.slice();
+      rawImg = new Float32Array(prevImg.length + newImg.length);
+      rawImg.set(prevImg);
+      rawImg.set(newImg, prevImg.length);
+      vols++;
+    }
+    if (voloffset === 0) break;
+    pos += 512; //possible to have multiple 512-byte lists of images
+  }
+  hdr.dims[4] = vols;
+  hdr.pixDims[4] = frame_duration[0];
+  if (vols > 1) {
+    hdr.dims[0] = 4;
+    let isFDvaries = false;
+    for (var i = 0; i < vols; i++)
+      if (frame_duration[i] !== frame_duration[0]) isFDvaries = true;
+    if (isFDvaries) console.log("Frame durations vary");
+  }
+  hdr.sform_code = 1;
+  hdr.affine = [
+    [-hdr.pixDims[1], 0, 0, (hdr.dims[1] - 2) * 0.5 * hdr.pixDims[1]],
+    [0, -hdr.pixDims[2], 0, (hdr.dims[2] - 2) * 0.5 * hdr.pixDims[2]],
+    [0, 0, -hdr.pixDims[3], (hdr.dims[3] - 2) * 0.5 * hdr.pixDims[3]],
+    [0, 0, 0, 1],
+  ];
+  hdr.numBitsPerVoxel = 32;
+  hdr.datatypeCode = this.DT_FLOAT;
+  return rawImg;
+}; // readECAT()
+
+NVImage.prototype.readV16 = function (buffer) {
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.dims = [3, 1, 1, 1, 0, 0, 0, 0];
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  var reader = new DataView(buffer);
+  hdr.dims[1] = reader.getUint16(0, true);
+  hdr.dims[2] = reader.getUint16(2, true);
+  hdr.dims[3] = reader.getUint16(4, true);
+  let nBytes = 2 * hdr.dims[1] * hdr.dims[2] * hdr.dims[3];
+  if (nBytes + 6 !== buffer.byteLength)
+    console.log("This does not look like a valid BrainVoyager V16 file");
+  hdr.numBitsPerVoxel = 16;
+  hdr.datatypeCode = this.DT_UINT16;
+  console.log("Warning: V16 files have no spatial transforms");
+  hdr.affine = [
+    [0, 0, -hdr.pixDims[1], (hdr.dims[1] - 2) * 0.5 * hdr.pixDims[1]],
+    [-hdr.pixDims[2], 0, 0, (hdr.dims[2] - 2) * 0.5 * hdr.pixDims[2]],
+    [0, -hdr.pixDims[3], 0, (hdr.dims[3] - 2) * 0.5 * hdr.pixDims[3]],
+    [0, 0, 0, 1],
+  ];
+  hdr.littleEndian = true;
+  return buffer.slice(6);
+}; // readV16()
+
+NVImage.prototype.readVMR = function (buffer) {
+  //https://support.brainvoyager.com/brainvoyager/automation-development/84-file-formats/343-developer-guide-2-6-the-format-of-vmr-files
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.dims = [3, 1, 1, 1, 0, 0, 0, 0];
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  var reader = new DataView(buffer);
+  let version = reader.getUint16(0, true);
+  if (version !== 4) console.log("Not a valid version 4 VMR image");
+  hdr.dims[1] = reader.getUint16(2, true);
+  hdr.dims[2] = reader.getUint16(4, true);
+  hdr.dims[3] = reader.getUint16(6, true);
+  let nBytes = hdr.dims[1] * hdr.dims[2] * hdr.dims[3];
+  if (version >= 4) {
+    let pos = 8 + nBytes; //offset to post header
+    let xoff = reader.getUint16(pos, true);
+    let yoff = reader.getUint16(pos + 2, true);
+    let zoff = reader.getUint16(pos + 4, true);
+    let framingCube = reader.getUint16(pos + 6, true);
+    let posInfo = reader.getUint32(pos + 8, true);
+    let coordSys = reader.getUint32(pos + 12, true);
+    let XmmStart = reader.getFloat32(pos + 16, true);
+    let YmmStart = reader.getFloat32(pos + 20, true);
+    let ZmmStart = reader.getFloat32(pos + 24, true);
+    let XmmEnd = reader.getFloat32(pos + 28, true);
+    let YmmEnd = reader.getFloat32(pos + 32, true);
+    let ZmmEnd = reader.getFloat32(pos + 36, true);
+    let Xsl = reader.getFloat32(pos + 40, true);
+    let Ysl = reader.getFloat32(pos + 44, true);
+    let Zsl = reader.getFloat32(pos + 48, true);
+    let colDirX = reader.getFloat32(pos + 52, true);
+    let colDirY = reader.getFloat32(pos + 56, true);
+    let colDirZ = reader.getFloat32(pos + 60, true);
+    let nRow = reader.getUint32(pos + 64, true);
+    let nCol = reader.getUint32(pos + 68, true);
+    let FOVrow = reader.getFloat32(pos + 72, true);
+    let FOVcol = reader.getFloat32(pos + 76, true);
+    let sliceThickness = reader.getFloat32(pos + 80, true);
+    let gapThickness = reader.getFloat32(pos + 84, true);
+    let nSpatialTransforms = reader.getUint32(pos + 88, true);
+    pos = pos + 92;
+    if (nSpatialTransforms > 0) {
+      let len = buffer.byteLength;
+      for (let i = 0; i < nSpatialTransforms; i++) {
+        //read variable length name name...
+        while (pos < len && reader.getUint8(pos) !== 0) pos++;
+        pos++;
+        let typ = reader.getUint32(pos, true);
+        pos += 4;
+        //read variable length name name...
+        while (pos < len && reader.getUint8(pos) !== 0) pos++;
+        pos++;
+        let nValues = reader.getUint32(pos, true);
+        pos += 4;
+        for (let j = 0; j < nValues; j++) pos += 4;
+      }
+    }
+    let LRconv = reader.getUint8(pos);
+    let ref = reader.getUint8(pos + 1);
+    hdr.pixDims[1] = reader.getFloat32(pos + 2, true);
+    hdr.pixDims[2] = reader.getFloat32(pos + 6, true);
+    hdr.pixDims[3] = reader.getFloat32(pos + 10, true);
+    let isVer = reader.getUint8(pos + 14);
+    let isTal = reader.getUint8(pos + 15);
+    let minInten = reader.getInt32(pos + 16, true);
+    let meanInten = reader.getInt32(pos + 20, true);
+    let maxInten = reader.getInt32(pos + 24, true);
+  }
+  console.log("Warning: VMR spatial transform not implemented");
+  //if (XmmStart === XmmEnd) { // https://brainvoyager.com/bv/sampledata/index.html??
+  hdr.affine = [
+    [0, 0, -hdr.pixDims[1], (hdr.dims[1] - 2) * 0.5 * hdr.pixDims[1]],
+    [-hdr.pixDims[2], 0, 0, (hdr.dims[2] - 2) * 0.5 * hdr.pixDims[2]],
+    [0, -hdr.pixDims[3], 0, (hdr.dims[3] - 2) * 0.5 * hdr.pixDims[3]],
+    [0, 0, 0, 1],
+  ];
+  //}
+  console.log(hdr);
+  hdr.numBitsPerVoxel = 8;
+  hdr.datatypeCode = this.DT_UNSIGNED_CHAR;
+  return buffer.slice(8, 8 + nBytes);
+}; // readVMR()
+
+NVImage.prototype.readMGH = function (buffer) {
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.dims = [3, 1, 1, 1, 0, 0, 0, 0];
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  var reader = new DataView(buffer);
+  var raw = buffer;
+  if (reader.getUint8(0) === 31 && reader.getUint8(1) === 139) {
+    var raw = fflate.decompressSync(new Uint8Array(buffer));
+    reader = new DataView(raw.buffer);
+  }
+  let version = reader.getInt32(0, false);
+  let width = reader.getInt32(4, false);
+  let height = reader.getInt32(8, false);
+  let depth = reader.getInt32(12, false);
+  let nframes = reader.getInt32(16, false);
+  let mtype = reader.getInt32(20, false);
+  let dof = reader.getInt32(24, false);
+  let goodRASFlag = reader.getInt16(28, false);
+  let spacingX = reader.getFloat32(30, false);
+  let spacingY = reader.getFloat32(34, false);
+  let spacingZ = reader.getFloat32(38, false);
+  let xr = reader.getFloat32(42, false);
+  let xa = reader.getFloat32(46, false);
+  let xs = reader.getFloat32(50, false);
+  let yr = reader.getFloat32(54, false);
+  let ya = reader.getFloat32(58, false);
+  let ys = reader.getFloat32(62, false);
+  let zr = reader.getFloat32(66, false);
+  let za = reader.getFloat32(70, false);
+  let zs = reader.getFloat32(74, false);
+  let cr = reader.getFloat32(78, false);
+  let ca = reader.getFloat32(82, false);
+  let cs = reader.getFloat32(86, false);
+  if (version !== 1 || mtype < 0 || mtype > 4)
+    console.log("Not a valid MGH file");
+  if (mtype === 0) {
+    hdr.numBitsPerVoxel = 8;
+    hdr.datatypeCode = this.DT_UNSIGNED_CHAR;
+  } else if (mtype === 4) {
+    hdr.numBitsPerVoxel = 16;
+    hdr.datatypeCode = this.DT_SIGNED_SHORT;
+  } else if (mtype === 1) {
+    hdr.numBitsPerVoxel = 32;
+    hdr.datatypeCode = this.DT_SIGNED_INT;
+  } else if (mtype === 3) {
+    hdr.numBitsPerVoxel = 32;
+    hdr.datatypeCode = this.DT_FLOAT;
+  }
+  hdr.dims[1] = width;
+  hdr.dims[2] = height;
+  hdr.dims[3] = depth;
+  hdr.dims[4] = nframes;
+  if (nframes > 1) hdr.dims[0] = 4;
+  hdr.pixDims[1] = spacingX;
+  hdr.pixDims[2] = spacingY;
+  hdr.pixDims[3] = spacingZ;
+  hdr.vox_offset = 284;
+  hdr.sform_code = 1;
+  let rot44 = mat4.fromValues(
+    xr * hdr.pixDims[1],
+    yr * hdr.pixDims[2],
+    zr * hdr.pixDims[3],
+    0,
+    xa * hdr.pixDims[1],
+    ya * hdr.pixDims[2],
+    za * hdr.pixDims[3],
+    0,
+    xs * hdr.pixDims[1],
+    ys * hdr.pixDims[2],
+    zs * hdr.pixDims[3],
+    0,
+    0,
+    0,
+    0,
+    1
+  );
+  let base = 0.0; //0 or 1: are voxels indexed from 0 or 1?
+  let Pcrs = [
+    hdr.dims[1] / 2.0 + base,
+    hdr.dims[2] / 2.0 + base,
+    hdr.dims[3] / 2.0 + base,
+    1,
+  ];
+  let PxyzOffset = [0, 0, 0, 0];
+  for (var i = 0; i < 3; i++) {
+    //multiply Pcrs * m
+    for (var j = 0; j < 3; j++) {
+      PxyzOffset[i] = PxyzOffset[i] + rot44[i + j * 4] * Pcrs[j];
+    }
+  }
+  hdr.affine = [
+    [rot44[0], rot44[1], rot44[2], PxyzOffset[0]],
+    [rot44[4], rot44[5], rot44[6], PxyzOffset[1]],
+    [rot44[8], rot44[9], rot44[10], PxyzOffset[2]],
+    [0, 0, 0, 1],
+  ];
+  let nBytes =
+    hdr.dims[1] *
+    hdr.dims[2] *
+    hdr.dims[3] *
+    hdr.dims[4] *
+    (hdr.numBitsPerVoxel / 8);
+  return raw.slice(hdr.vox_offset, hdr.vox_offset + nBytes);
+}; // readMGH()
+
+NVImage.prototype.readHEAD = function (dataBuffer, pairedImgData) {
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.dims[0] = 3;
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  let orientSpecific = [0, 0, 0];
+  let xyzOrigin = [0, 0, 0];
+  let xyzDelta = [1, 1, 1];
+  let txt = new TextDecoder().decode(dataBuffer);
+  var lines = txt.split("\n");
+  let nlines = lines.length;
+  let i = 0;
+  let hasIJK_TO_DICOM_REAL = false;
+  while (i < nlines) {
+    let line = lines[i]; //e.g. 'type = string-attribute'
+    i++;
+    if (!line.startsWith("type")) continue; //n.b. white space varies, "type =" vs "type  ="
+    let isInt = line.includes("integer-attribute");
+    let isFloat = line.includes("float-attribute");
+    line = lines[i]; //e.g. 'name = IDCODE_DATE'
+    i++;
+    if (!line.startsWith("name")) continue;
+    let items = line.split("= ");
+    let key = items[1]; //e.g. 'IDCODE_DATE'
+    line = lines[i]; //e.g. 'count = 5'
+    i++;
+    items = line.split("= ");
+    let count = parseInt(items[1]); //e.g. '5'
+    if (count < 1) continue;
+    line = lines[i]; //e.g. ''LSB_FIRST~'
+    i++;
+    items = line.trim().split(/\s+/);
+    if (isFloat || isInt) {
+      //read arrays written on multiple lines
+      while (items.length < count) {
+        line = lines[i]; //e.g. ''LSB_FIRST~'
+        i++;
+        let items2 = line.trim().split(/\s+/);
+        items.push(...items2);
+      }
+      for (var j = 0; j < count; j++) items[j] = parseFloat(items[j]);
+    }
+    switch (key) {
+      case "BYTEORDER_STRING":
+        if (items[0].includes("LSB_FIRST")) hdr.littleEndian = true;
+        else if (items[0].includes("MSB_FIRST")) hdr.littleEndian = false;
+        break;
+      case "BRICK_TYPES":
+        hdr.dims[4] = count;
+        let datatype = parseInt(items[0]);
+        if (datatype === 0) {
+          hdr.numBitsPerVoxel = 8;
+          hdr.datatypeCode = this.DT_UNSIGNED_CHAR;
+        } else if (datatype === 1) {
+          hdr.numBitsPerVoxel = 16;
+          hdr.datatypeCode = this.DT_SIGNED_SHORT;
+        } else if (datatype === 1) {
+          hdr.numBitsPerVoxel = 32;
+          hdr.datatypeCode = this.DT_FLOAT;
+        } else console.log("Unknown BRICK_TYPES ", datatype);
+        break;
+      case "IJK_TO_DICOM_REAL":
+        if (count < 12) break;
+        hasIJK_TO_DICOM_REAL = true;
+        hdr.sform_code = 2;
+        //note DICOM space is LPS while NIfTI is RAS
+        hdr.affine = [
+          [-items[0], -items[1], -items[2], -items[3]],
+          [-items[4], -items[5], -items[6], -items[7]],
+          [items[8], items[9], items[10], items[11]],
+          [0, 0, 0, 1],
+        ];
+        break;
+      case "DATASET_DIMENSIONS":
+        count = Math.max(count, 3);
+        for (var j = 0; j < count; j++) hdr.dims[j + 1] = items[j];
+        break;
+      case "ORIENT_SPECIFIC":
+        orientSpecific = items;
+        break;
+      case "ORIGIN":
+        xyzOrigin = items;
+        break;
+      case "DELTA":
+        xyzDelta = items;
+        break;
+      case "TAXIS_FLOATS":
+        hdr.pixDims[4] = items[0];
+        break;
+      default:
+      //console.log('Unknown:',key);
+    } //read item
+  } //read all lines
+  if (!hasIJK_TO_DICOM_REAL)
+    this.THD_daxes_to_NIFTI(xyzDelta, xyzOrigin, orientSpecific);
+  else this.SetPixDimFromSForm();
+  let nBytes =
+    (hdr.numBitsPerVoxel / 8) *
+    hdr.dims[1] *
+    hdr.dims[2] *
+    hdr.dims[3] *
+    hdr.dims[4];
+  if (pairedImgData.byteLength < nBytes) {
+    //n.b. npm run dev implicitly extracts gz, npm run demo does not!
+    //assume gz compressed
+    var raw = fflate.decompressSync(new Uint8Array(pairedImgData));
+    return raw.buffer;
+  }
+  return pairedImgData.slice();
+};
+
+NVImage.prototype.readMHA = function (buffer, pairedImgData) {
+  //https://itk.org/Wiki/ITK/MetaIO/Documentation#Reading_a_Brick-of-Bytes_.28an_N-Dimensional_volume_in_a_single_file.29
+  let len = buffer.byteLength;
+  if (len < 20)
+    throw new Error("File too small to be VTK: bytes = " + buffer.byteLength);
+  var bytes = new Uint8Array(buffer);
+  let pos = 0;
+  function readStr() {
+    while (pos < len && bytes[pos] === 10) pos++; //skip blank lines
+    let startPos = pos;
+    while (pos < len && bytes[pos] !== 10) pos++;
+    pos++; //skip EOLN
+    if (pos - startPos < 1) return "";
+    return new TextDecoder().decode(buffer.slice(startPos, pos - 1));
+  }
+  let line = readStr(); //1st line: signature
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.littleEndian = true;
+  let isGz = false;
+  let isDetached = false;
+  let compressedDataSize = 0;
+  let mat33 = mat3.fromValues(NaN, 0, 0, 0, 1, 0, 0, 0, 1);
+  let offset = vec3.fromValues(0, 0, 0);
+  while (line !== "") {
+    let items = line.split(" ");
+    if (items.length > 2);
+    items = items.slice(2);
+    if (line.startsWith("BinaryDataByteOrderMSB") && items[0].includes("False"))
+      hdr.littleEndian = true;
+    if (line.startsWith("BinaryDataByteOrderMSB") && items[0].includes("True"))
+      hdr.littleEndian = false;
+    if (line.startsWith("CompressedData") && items[0].includes("True"))
+      isGz = true;
+    if (line.startsWith("CompressedDataSize"))
+      compressedDataSize = parseInt(items[0]);
+    if (line.startsWith("TransformMatrix")) {
+      for (var d = 0; d < 9; d++) mat33[d] = parseFloat(items[d]);
+    }
+    if (line.startsWith("Offset")) {
+      offset[0] = parseFloat(items[0]);
+      offset[1] = parseFloat(items[1]);
+      offset[2] = parseFloat(items[2]);
+    }
+    //if (line.startsWith("AnatomicalOrientation")) //we can ignore, tested with Slicer3D converting NIfTIspace images
+    if (line.startsWith("ElementSpacing")) {
+      hdr.pixDims[1] = parseFloat(items[0]);
+      hdr.pixDims[2] = parseFloat(items[1]);
+      hdr.pixDims[3] = parseFloat(items[2]);
+      if (items.length > 3) hdr.pixDims[4] = parseFloat(items[3]);
+    }
+    if (line.startsWith("DimSize")) {
+      hdr.dims[0] = items.length;
+      for (var d = 0; d < items.length; d++)
+        hdr.dims[d + 1] = parseInt(items[d]);
+    }
+    if (line.startsWith("ElementType")) {
+      switch (items[0]) {
+        case "MET_UCHAR":
+          hdr.numBitsPerVoxel = 8;
+          hdr.datatypeCode = this.DT_UNSIGNED_CHAR;
+          break;
+        case "MET_CHAR":
+          hdr.numBitsPerVoxel = 8;
+          hdr.datatypeCode = this.DT_INT8;
+          break;
+        case "MET_SHORT":
+          hdr.numBitsPerVoxel = 16;
+          hdr.datatypeCode = this.DT_SIGNED_SHORT;
+          break;
+        case "MET_USHORT":
+          hdr.numBitsPerVoxel = 16;
+          hdr.datatypeCode = this.DT_UINT16;
+          break;
+        case "MET_INT":
+          hdr.numBitsPerVoxel = 32;
+          hdr.datatypeCode = this.DT_SIGNED_INT;
+          break;
+        case "MET_UINT":
+          hdr.numBitsPerVoxel = 32;
+          hdr.datatypeCode = this.DT_UINT32;
+          break;
+        case "MET_FLOAT":
+          hdr.numBitsPerVoxel = 32;
+          hdr.datatypeCode = this.DT_FLOAT;
+          break;
+        case "MET_DOUBLE":
+          hdr.numBitsPerVoxel = 64;
+          hdr.datatypeCode = this.DT_DOUBLE;
+          break;
+        default:
+          throw new Error("Unsupported NRRD data type: " + value);
+      }
+    }
+    if (line.startsWith("ObjectType") && !items[0].includes("Image"))
+      console.log("Only able to read ObjectType = Image, not " + line);
+    if (line.startsWith("ElementDataFile")) {
+      if (items[0] !== "LOCAL") isDetached = true;
+      break;
+    }
+    line = readStr();
+  }
+  let mmMat = mat3.fromValues(
+    hdr.pixDims[1],
+    0,
+    0,
+    0,
+    hdr.pixDims[2],
+    0,
+    0,
+    0,
+    hdr.pixDims[3]
+  );
+  mat3.multiply(mat33, mmMat, mat33);
+  hdr.affine = [
+    [-mat33[0], -mat33[3], -mat33[6], -offset[0]],
+    [-mat33[1], -mat33[4], -mat33[7], -offset[1]],
+    [mat33[2], mat33[5], mat33[8], offset[2]],
+    [0, 0, 0, 1],
+  ];
+  hdr.vox_offset = pos;
+  if (isDetached && pairedImgData) {
+    if (isGz)
+      return fflate.decompressSync(new Uint8Array(buffer.slice(hdr.vox_offset)))
+        .buffer;
+    return pairedImgData.slice();
+  }
+  if (isGz)
+    return fflate.decompressSync(new Uint8Array(buffer.slice(hdr.vox_offset)))
+      .buffer;
+  return buffer.slice(hdr.vox_offset);
+}; //readMHA()
+
+NVImage.prototype.readMIF = function (buffer, pairedImgData) {
+  //https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html#mrtrix-image-formats
+  //MIF files typically 3D (e.g. anatomical), 4D (fMRI, DWI). 5D rarely seen
+  //This read currently supports up to 5D. To create test: "mrcat -axis 4 a4d.mif b4d.mif out5d.mif"
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  hdr.dims = [1, 1, 1, 1, 1, 1, 1, 1];
+  let len = buffer.byteLength;
+  if (len < 20) throw new Error("File too small to be MIF: bytes = " + len);
+  var bytes = new Uint8Array(buffer);
+  if (bytes[0] === 31 && bytes[1] === 139) {
+    console.log("MIF with GZ decompression");
+    var raw = fflate.decompressSync(new Uint8Array(buffer));
+    buffer = raw.buffer;
+    len = buffer.byteLength;
+  }
+  let pos = 0;
+  function readStr() {
+    while (pos < len && bytes[pos] === 10) pos++; //skip blank lines
+    let startPos = pos;
+    while (pos < len && bytes[pos] !== 10) pos++;
+    pos++; //skip EOLN
+    if (pos - startPos < 1) return "";
+    return new TextDecoder().decode(buffer.slice(startPos, pos - 1));
+  }
+  let line = readStr(); //1st line: signature 'mrtrix tracks'
+  if (!line.startsWith("mrtrix image")) {
+    console.log("Not a valid MIF file");
+    return;
+  }
+  let layout = [];
+  let nTransform = 0;
+  let TR = 0;
+  let isDetached = false;
+  line = readStr();
+  while (pos < len && !line.startsWith("END")) {
+    let items = line.split(":"); // "vox: 1,1,1" -> "vox", " 1,1,1"
+    line = readStr();
+    if (items.length < 2) break; //
+    let tag = items[0]; // "datatype", "dim"
+    items = items[1].split(","); // " 1,1,1" -> " 1", "1", "1"
+    for (let i = 0; i < items.length; i++) items[i] = items[i].trim(); // " 1", "1", "1" -> "1", "1", "1"
+    switch (tag) {
+      case "dim":
+        hdr.dims[0] = items.length;
+        for (let i = 0; i < items.length; i++)
+          hdr.dims[i + 1] = parseInt(items[i]);
+        break;
+      case "vox":
+        for (let i = 0; i < items.length; i++) {
+          hdr.pixDims[i + 1] = parseFloat(items[i]);
+          if (isNaN(hdr.pixDims[i + 1])) hdr.pixDims[i + 1] = 0.0;
+        }
+        break;
+      case "layout":
+        for (let i = 0; i < items.length; i++) layout.push(parseInt(items[i])); //n.b. JavaScript preserves sign for -0
+        break;
+      case "datatype":
+        let dt = items[0];
+        if (dt.startsWith("Int8")) hdr.datatypeCode = this.DT_INT8;
+        else if (dt.startsWith("UInt8"))
+          hdr.datatypeCode = this.DT_UNSIGNED_CHAR;
+        else if (dt.startsWith("Int16"))
+          hdr.datatypeCode = this.DT_SIGNED_SHORT;
+        else if (dt.startsWith("UInt16")) hdr.datatypeCode = this.DT_UINT16;
+        else if (dt.startsWith("Int32")) hdr.datatypeCode = this.DT_SIGNED_INT;
+        else if (dt.startsWith("UInt32")) hdr.datatypeCode = this.DT_UINT32;
+        else if (dt.startsWith("Float32")) hdr.datatypeCode = this.DT_FLOAT;
+        else if (dt.startsWith("Float64")) hdr.datatypeCode = this.DT_DOUBLE;
+        else console.log("Unsupported datatype " + dt);
+        if (dt.includes("8")) hdr.numBitsPerVoxel = 8;
+        else if (dt.includes("16")) hdr.numBitsPerVoxel = 16;
+        else if (dt.includes("32")) hdr.numBitsPerVoxel = 32;
+        else if (dt.includes("64")) hdr.numBitsPerVoxel = 64;
+        hdr.littleEndian = true; //native, to do support big endian readers
+        if (dt.endsWith("LE")) hdr.littleEndian = true;
+        if (dt.endsWith("BE")) hdr.littleEndian = false;
+        break;
+      case "transform":
+        if (nTransform > 2 || items.length !== 4) break;
+        hdr.affine[nTransform][0] = parseFloat(items[0]);
+        hdr.affine[nTransform][1] = parseFloat(items[1]);
+        hdr.affine[nTransform][2] = parseFloat(items[2]);
+        hdr.affine[nTransform][3] = parseFloat(items[3]);
+        nTransform++;
+        break;
+      case "RepetitionTime":
+        TR = parseFloat(items[0]);
+        break;
+      case "file":
+        isDetached = !items[0].startsWith(". ");
+        if (!isDetached) {
+          items = items[0].split(" "); //". 2336" -> ". ", "2336"
+          hdr.vox_offset = parseInt(items[1]);
+        }
+        break;
+    }
+  }
+  let ndim = hdr.dims[0];
+  if (ndim > 5)
+    console.log("reader only designed for a maximum of 5 dimensions (XYZTD)");
+  let nvox = 1;
+  for (let i = 0; i < ndim; i++) nvox *= Math.max(hdr.dims[i + 1], 1);
+  console.log(nvox);
+  //let nvox = hdr.dims[1] * hdr.dims[2] * hdr.dims[3] * hdr.dims[4];
+  for (let i = 0; i < 3; i++) {
+    for (let j = 0; j < 3; j++) {
+      //hdr.affine[i][j] *= hdr.pixDims[i + 1];
+      hdr.affine[i][j] *= hdr.pixDims[j + 1];
+    }
+  }
+  console.log("mif affine:" + hdr.affine[0]);
+  if (TR > 0) hdr.pixDims[4] = TR;
+  if (isDetached && !pairedImgData)
+    console.log("MIH header provided without paired image data");
+  let rawImg = [];
+  if (isDetached) rawImg = pairedImgData.slice();
+  //n.b. mrconvert can pad files? See dtitest_Siemens_SC 4_dti_nopf_x2_pitch
+  else
+    rawImg = buffer.slice(
+      hdr.vox_offset,
+      hdr.vox_offset + nvox * (hdr.numBitsPerVoxel / 8)
+    );
+  if (layout.length != hdr.dims[0]) console.log("dims does not match layout");
+  //estimate strides:
+  let stride = 1;
+  let instride = [1, 1, 1, 1, 1];
+  let inflip = [false, false, false, false, false];
+  for (let i = 0; i < layout.length; i++) {
+    for (let j = 0; j < layout.length; j++) {
+      let a = Math.abs(layout[j]);
+      if (a != i) continue;
+      instride[j] = stride;
+      //detect -0: https://medium.com/coding-at-dawn/is-negative-zero-0-a-number-in-javascript-c62739f80114
+      if (layout[j] < 0 || Object.is(layout[j], -0)) inflip[j] = true;
+      stride *= hdr.dims[j + 1];
+    }
+  }
+  //lookup table for flips and stride offsets:
+  const range = (start, stop, step) =>
+    Array.from(
+      { length: (stop - start) / step + 1 },
+      (_, i) => start + i * step
+    );
+  let xlut = range(0, hdr.dims[1] - 1, 1);
+  if (inflip[0]) xlut = range(hdr.dims[1] - 1, 0, -1);
+  for (let i = 0; i < hdr.dims[1]; i++) xlut[i] *= instride[0];
+  let ylut = range(0, hdr.dims[2] - 1, 1);
+  if (inflip[1]) ylut = range(hdr.dims[2] - 1, 0, -1);
+  for (let i = 0; i < hdr.dims[2]; i++) ylut[i] *= instride[1];
+  let zlut = range(0, hdr.dims[3] - 1, 1);
+  if (inflip[2]) zlut = range(hdr.dims[3] - 1, 0, -1);
+  for (let i = 0; i < hdr.dims[3]; i++) zlut[i] *= instride[2];
+  let tlut = range(0, hdr.dims[4] - 1, 1);
+  if (inflip[3]) tlut = range(hdr.dims[4] - 1, 0, -1);
+  for (let i = 0; i < hdr.dims[4]; i++) tlut[i] *= instride[3];
+  let dlut = range(0, hdr.dims[5] - 1, 1);
+  if (inflip[4]) dlut = range(hdr.dims[5] - 1, 0, -1);
+  for (let i = 0; i < hdr.dims[5]; i++) dlut[i] *= instride[4];
+  //input and output arrays
+  let j = 0;
+  let inVs = [];
+  let outVs = [];
+  if (hdr.numBitsPerVoxel === 8) {
+    inVs = new Uint8Array(rawImg);
+    outVs = new Uint8Array(nvox);
+  } //8bit
+  if (hdr.numBitsPerVoxel === 16) {
+    inVs = new Uint16Array(rawImg);
+    outVs = new Uint16Array(nvox);
+  }
+  if (hdr.numBitsPerVoxel === 32) {
+    inVs = new Uint32Array(rawImg);
+    outVs = new Uint32Array(nvox);
+  } //32bit
+  if (hdr.numBitsPerVoxel === 64) {
+    inVs = new BigUint64Array(rawImg);
+    outVs = new BigUint64Array(nvox);
+  } //64bit
+  for (let d = 0; d < hdr.dims[5]; d++) {
+    for (let t = 0; t < hdr.dims[4]; t++) {
+      for (let z = 0; z < hdr.dims[3]; z++) {
+        for (let y = 0; y < hdr.dims[2]; y++) {
+          for (let x = 0; x < hdr.dims[1]; x++) {
+            outVs[j] = inVs[xlut[x] + ylut[y] + zlut[z] + tlut[t] + dlut[d]];
+            j++;
+          } //for x
+        } //for y
+      } //for z
+    } //for t (time)
+  } // for d (direction, phase/real, etc)
+  return outVs;
+}; // readMIF()
+
+NVImage.prototype.readNRRD = function (dataBuffer, pairedImgData) {
+  //inspired by parserNRRD.js in https://github.com/xtk
+  //Copyright (c) 2012 The X Toolkit Developers <dev@goXTK.com>
+  // http://www.opensource.org/licenses/mit-license.php
+  this.hdr = new nifti.NIFTI1();
+  let hdr = this.hdr;
+  hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0];
+  let len = dataBuffer.byteLength;
+  //extract initial text header
+  var txt = null;
+  var bytes = new Uint8Array(dataBuffer);
+  for (var i = 1; i < len; i++) {
+    if (bytes[i - 1] == 10 && bytes[i] == 10) {
+      let v = dataBuffer.slice(0, i - 1);
+      txt = new TextDecoder().decode(v);
+      hdr.vox_offset = i + 1;
+      break;
+    }
+  }
+  var lines = txt.split("\n");
+  if (!lines[0].startsWith("NRRD")) alert("Invalid NRRD image");
+  var n = lines.length;
+  let isGz = false;
+  let isMicron = false;
+  let isDetached = false;
+  let mat33 = mat3.fromValues(NaN, 0, 0, 0, 1, 0, 0, 0, 1);
+  let offset = vec3.fromValues(0, 0, 0);
+  let rot33 = mat3.create();
+  for (let i = 1; i < n; i++) {
+    let str = lines[i];
+    if (str[0] === "#") continue; //comment
+    str = str.toLowerCase();
+    let items = str.split(":");
+    if (items.length < 2) continue;
+    let key = items[0].trim();
+    let value = items[1].trim();
+    value = value.replaceAll(")", " ");
+    value = value.replaceAll("(", " ");
+    value = value.trim();
+    switch (key) {
+      case "data file":
+        isDetached = true;
+        break;
+      case "encoding":
+        if (value.includes("raw")) isGz = false;
+        else if (value.includes("gz")) isGz = true;
+        else alert("Unsupported NRRD encoding");
+        break;
+      case "type":
+        switch (value) {
+          case "uchar":
+          case "unsigned char":
+          case "uint8":
+          case "uint8_t":
+            hdr.numBitsPerVoxel = 8;
+            hdr.datatypeCode = this.DT_UNSIGNED_CHAR;
+            break;
+          case "signed char":
+          case "int8":
+          case "int8_t":
+            hdr.numBitsPerVoxel = 8;
+            hdr.datatypeCode = this.DT_INT8;
+            break;
+          case "short":
+          case "short int":
+          case "signed short":
+          case "signed short int":
+          case "int16":
+          case "int16_t":
+            hdr.numBitsPerVoxel = 16;
+            hdr.datatypeCode = this.DT_SIGNED_SHORT;
+            break;
+          case "ushort":
+          case "unsigned short":
+          case "unsigned short int":
+          case "uint16":
+          case "uint16_t":
+            hdr.numBitsPerVoxel = 16;
+            hdr.datatypeCode = this.DT_UINT16;
+            break;
+          case "int":
+          case "signed int":
+          case "int32":
+          case "int32_t":
+            hdr.numBitsPerVoxel = 32;
+            hdr.datatypeCode = this.DT_SIGNED_INT;
+            break;
+          case "uint":
+          case "unsigned int":
+          case "uint32":
+          case "uint32_t":
+            hdr.numBitsPerVoxel = 32;
+            hdr.datatypeCode = this.DT_UINT32;
+            break;
+          case "float":
+            hdr.numBitsPerVoxel = 32;
+            hdr.datatypeCode = this.DT_FLOAT;
+            break;
+          case "double":
+            hdr.numBitsPerVoxel = 64;
+            hdr.datatypeCode = this.DT_DOUBLE;
+            break;
+          default:
+            throw new Error("Unsupported NRRD data type: " + value);
+        }
+        break;
+      case "spacings":
+        let pixdims = value.split(/[ ,]+/);
+        for (var d = 0; d < pixdims.length; d++)
+          hdr.pixDims[d + 1] = parseFloat(dims[d]);
+      case "sizes":
+        let dims = value.split(/[ ,]+/);
+        hdr.dims[0] = dims.length;
+        for (let d = 0; d < dims.length; d++)
+          hdr.dims[d + 1] = parseInt(dims[d]);
+        break;
+      case "endian":
+        if (value.includes("little")) hdr.littleEndian = true;
+        else if (value.includes("big")) hdr.littleEndian = false;
+        break;
+      case "space directions":
+        let vs = value.split(/[ ,]+/);
+        if (vs.length !== 9) break;
+        for (var d = 0; d < 9; d++) mat33[d] = parseFloat(vs[d]);
+        break;
+      case "space origin":
+        let ts = value.split(/[ ,]+/);
+        if (ts.length !== 3) break;
+        offset[0] = parseFloat(ts[0]);
+        offset[1] = parseFloat(ts[1]);
+        offset[2] = parseFloat(ts[2]);
+        break;
+      case "space units":
+        if (value.includes("microns")) isMicron = true;
+        break;
+      case "space":
+        if (value.includes("right-anterior-superior") || value.includes("RAS"))
+          rot33 = mat3.fromValues(
+            1,
+            0,
+            0,
+
+            0,
+            1,
+            0,
+
+            0,
+            0,
+            1
+          );
+        else if (
+          value.includes("left-anterior-superior") ||
+          value.includes("LAS")
+        )
+          rot33 = mat3.fromValues(
+            -1,
+            0,
+            0,
+
+            0,
+            1,
+            0,
+
+            0,
+            0,
+            1
+          );
+        else if (
+          value.includes("left-posterior-superior") ||
+          value.includes("LPS")
+        )
+          rot33 = mat3.fromValues(
+            -1,
+            0,
+            0,
+
+            0,
+            -1,
+            0,
+
+            0,
+            0,
+            1
+          );
+        else console.log("Unsupported NRRD space value:", value);
+        break;
+      default:
+      //console.log('Unknown:',key);
+    } //read line
+  } //read all lines
+  if (!isNaN(mat33[0])) {
+    //if spatial transform provided
+    this.hdr.sform_code = 2;
+    if (isMicron) {
+      //convert micron to mm
+      mat4.multiplyScalar(mat33, mat33, 0.001);
+      offset[0] *= 0.001;
+      offset[1] *= 0.001;
+      offset[2] *= 0.001;
+    }
+    if (rot33[0] < 0) offset[0] = -offset[0]; //origin L<->R
+    if (rot33[4] < 0) offset[1] = -offset[1]; //origin A<->P
+    if (rot33[8] < 0) offset[2] = -offset[2]; //origin S<->I
+    mat3.multiply(mat33, rot33, mat33);
+    let mat = mat4.fromValues(
+      mat33[0],
+      mat33[3],
+      mat33[6],
+      offset[0],
+      mat33[1],
+      mat33[4],
+      mat33[7],
+      offset[1],
+      mat33[2],
+      mat33[5],
+      mat33[8],
+      offset[2],
+      0,
+      0,
+      0,
+      1
+    );
+    let mm000 = this.vox2mm([0, 0, 0], mat);
+    let mm100 = this.vox2mm([1, 0, 0], mat);
+    vec3.subtract(mm100, mm100, mm000);
+    let mm010 = this.vox2mm([0, 1, 0], mat);
+    vec3.subtract(mm010, mm010, mm000);
+    let mm001 = this.vox2mm([0, 0, 1], mat);
+    vec3.subtract(mm001, mm001, mm000);
+    hdr.pixDims[1] = vec3.length(mm100);
+    hdr.pixDims[2] = vec3.length(mm010);
+    hdr.pixDims[3] = vec3.length(mm001);
+    hdr.affine = [
+      [mat[0], mat[1], mat[2], mat[3]],
+      [mat[4], mat[5], mat[6], mat[7]],
+      [mat[8], mat[9], mat[10], mat[11]],
+      [0, 0, 0, 1],
+    ];
+  }
+
+  let nvox = hdr.dims[1] * hdr.dims[2] * hdr.dims[3];
+  if (isDetached && pairedImgData) {
+    //??? .gz files automatically decompressed?
+    return pairedImgData.slice();
+  }
+  if (isDetached)
+    console.log(
+      "Missing data: NRRD header describes detached data file but only one URL provided"
+    );
+  if (isGz)
+    return fflate.decompressSync(
+      new Uint8Array(dataBuffer.slice(hdr.vox_offset))
+    ).buffer;
+  else return dataBuffer.slice(hdr.vox_offset);
+}; //readNRRD()
+
 // not included in public docs
 NVImage.prototype.calculateRAS = function () {
   //Transform to orient NIfTI image to Left->Right,Posterior->Anterior,Inferior->Superior (48 possible permutations)
@@ -282,7 +1693,7 @@ NVImage.prototype.calculateRAS = function () {
   // not elegant, as JavaScript arrays are always 1D
   let a = this.hdr.affine;
   let header = this.hdr;
-  let absR = mat.mat3.fromValues(
+  let absR = mat3.fromValues(
     Math.abs(a[0][0]),
     Math.abs(a[0][1]),
     Math.abs(a[0][2]),
@@ -330,7 +1741,7 @@ NVImage.prototype.calculateRAS = function () {
   perm[ixyz[0] - 1] = 1;
   perm[ixyz[1] - 1] = 2;
   perm[ixyz[2] - 1] = 3;
-  let rotM = mat.mat4.fromValues(
+  let rotM = mat4.fromValues(
     a[0][0],
     a[0][1],
     a[0][2],
@@ -353,23 +1764,17 @@ NVImage.prototype.calculateRAS = function () {
   this.mm100 = this.vox2mm([header.dims[1] - 0.5, -0.5, -0.5], rotM);
   this.mm010 = this.vox2mm([-0.5, header.dims[2] - 0.5, -0.5], rotM);
   this.mm001 = this.vox2mm([-0.5, -0.5, header.dims[3] - 0.5], rotM);
-  let R = mat.mat4.create();
-  mat.mat4.copy(R, rotM);
+  let R = mat4.create();
+  mat4.copy(R, rotM);
   for (let i = 0; i < 3; i++) {
     for (let j = 0; j < 3; j++) {
       R[i * 4 + j] = rotM[i * 4 + perm[j] - 1]; //rotM[i+(4*(perm[j]-1))];//rotM[i],[perm[j]-1];
     }
   }
   let flip = [0, 0, 0];
-  if (R[0] < 0) {
-    flip[0] = 1; //R[0][0]
-  }
-  if (R[5] < 0) {
-    flip[1] = 1; //R[1][1]
-  }
-  if (R[10] < 0) {
-    flip[2] = 1; //R[2][2]
-  }
+  if (R[0] < 0) flip[0] = 1; //R[0][0]
+  if (R[5] < 0) flip[1] = 1; //R[1][1]
+  if (R[10] < 0) flip[2] = 1; //R[2][2]
   this.dimsRAS = [
     header.dims[0],
     header.dims[perm[0]],
@@ -382,31 +1787,34 @@ NVImage.prototype.calculateRAS = function () {
     header.pixDims[perm[1]],
     header.pixDims[perm[2]],
   ];
+  this.permRAS = perm.slice();
+  for (let i = 0; i < 3; i++)
+    if (flip[i] === 1) this.permRAS[i] = -this.permRAS[i];
   if (this.arrayEquals(perm, [1, 2, 3]) && this.arrayEquals(flip, [0, 0, 0])) {
-    this.toRAS = mat.mat4.create(); //aka fromValues(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1);
-    this.matRAS = mat.mat4.clone(rotM);
+    this.toRAS = mat4.create(); //aka fromValues(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1);
+    this.matRAS = mat4.clone(rotM);
     this.calculateOblique();
     return; //no rotation required!
   }
-  mat.mat4.identity(rotM);
+  mat4.identity(rotM);
   rotM[0 + 0 * 4] = 1 - flip[0] * 2;
   rotM[1 + 1 * 4] = 1 - flip[1] * 2;
   rotM[2 + 2 * 4] = 1 - flip[2] * 2;
   rotM[3 + 0 * 4] = (header.dims[perm[0]] - 1) * flip[0];
   rotM[3 + 1 * 4] = (header.dims[perm[1]] - 1) * flip[1];
   rotM[3 + 2 * 4] = (header.dims[perm[2]] - 1) * flip[2];
-  let residualR = mat.mat4.create();
-  mat.mat4.invert(residualR, rotM);
-  mat.mat4.multiply(residualR, residualR, R);
-  this.matRAS = mat.mat4.clone(residualR);
-  rotM = mat.mat4.fromValues(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1);
+  let residualR = mat4.create();
+  mat4.invert(residualR, rotM);
+  mat4.multiply(residualR, residualR, R);
+  this.matRAS = mat4.clone(residualR);
+  rotM = mat4.fromValues(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1);
   rotM[perm[0] - 1 + 0 * 4] = -flip[0] * 2 + 1;
   rotM[perm[1] - 1 + 1 * 4] = -flip[1] * 2 + 1;
   rotM[perm[2] - 1 + 2 * 4] = -flip[2] * 2 + 1;
   rotM[3 + 0 * 4] = flip[0];
   rotM[3 + 1 * 4] = flip[1];
   rotM[3 + 2 * 4] = flip[2];
-  this.toRAS = mat.mat4.clone(rotM);
+  this.toRAS = mat4.clone(rotM);
   log.debug(this.hdr.dims);
   log.debug(this.dimsRAS);
   this.calculateOblique();
@@ -414,22 +1822,22 @@ NVImage.prototype.calculateRAS = function () {
 
 // not included in public docs
 NVImage.prototype.vox2mm = function (XYZ, mtx) {
-  let sform = mat.mat4.clone(mtx);
-  mat.mat4.transpose(sform, sform);
-  let pos = mat.vec4.fromValues(XYZ[0], XYZ[1], XYZ[2], 1);
-  mat.vec4.transformMat4(pos, pos, sform);
-  let pos3 = mat.vec3.fromValues(pos[0], pos[1], pos[2]);
+  let sform = mat4.clone(mtx);
+  mat4.transpose(sform, sform);
+  let pos = vec4.fromValues(XYZ[0], XYZ[1], XYZ[2], 1);
+  vec4.transformMat4(pos, pos, sform);
+  let pos3 = vec3.fromValues(pos[0], pos[1], pos[2]);
   return pos3;
 }; // vox2mm()
 
 NVImage.prototype.mm2vox = function (mm) {
-  let sform = mat.mat4.fromValues(...this.hdr.affine.flat());
-  let out = mat.mat4.clone(sform);
-  mat.mat4.transpose(out, sform);
-  mat.mat4.invert(out, out);
-  let pos = mat.vec4.fromValues(mm[0], mm[1], mm[2], 1);
-  mat.vec4.transformMat4(pos, pos, out);
-  let pos3 = mat.vec3.fromValues(pos[0], pos[1], pos[2]);
+  let sform = mat4.fromValues(...this.hdr.affine.flat());
+  let out = mat4.clone(sform);
+  mat4.transpose(out, sform);
+  mat4.invert(out, out);
+  let pos = vec4.fromValues(mm[0], mm[1], mm[2], 1);
+  vec4.transformMat4(pos, pos, out);
+  let pos3 = vec3.fromValues(pos[0], pos[1], pos[2]);
   return [Math.round(pos3[0]), Math.round(pos3[1]), Math.round(pos3[2])];
 }; // vox2mm()
 
@@ -459,12 +1867,32 @@ NVImage.prototype.colorMaps = function (sort = true) {
   return sort === true ? cm.sort() : cm;
 };
 
+NVImage.prototype.setColorMap = function (cm) {
+  let allColorMaps = this.colorMaps();
+  if (allColorMaps.indexOf(cm.toLowerCase()) !== -1) {
+    this.colorMap = cm.toLowerCase();
+    this.calMinMax();
+  } else {
+    log.warn(`color map ${cm} is not a valid color map`);
+  }
+};
+
 // not included in public docs
 // given an overlayItem and its img TypedArray, calculate 2% and 98% display range if needed
 //clone FSL robust_range estimates https://github.com/rordenlab/niimath/blob/331758459140db59290a794350d0ff3ad4c37b67/src/core32.c#L1215
 //ToDo: convert to web assembly, this is slow in JavaScript
 NVImage.prototype.calMinMax = function () {
+  let cm = this.colorMap;
+  let allColorMaps = this.colorMaps();
+  let cmMin = 0;
+  let cmMax = 0;
+  if (allColorMaps.indexOf(cm.toLowerCase()) !== -1) {
+    cmMin = cmaps[cm.toLowerCase()].min;
+    cmMax = cmaps[cm.toLowerCase()].max;
+  }
+
   if (
+    cmMin === cmMax &&
     this.trustCalMinMax &&
     isFinite(this.hdr.cal_min) &&
     isFinite(this.hdr.cal_max) &&
@@ -483,16 +1911,6 @@ NVImage.prototype.calMinMax = function () {
       this.hdr.cal_max,
     ];
   }
-
-  let cm = this.colorMap;
-  let allColorMaps = this.colorMaps();
-  let cmMin = 0;
-  let cmMax = 0;
-  if (allColorMaps.indexOf(cm.toLowerCase()) != -1) {
-    cmMin = cmaps[cm.toLowerCase()].min;
-    cmMax = cmaps[cm.toLowerCase()].max;
-  }
-
   // if color map specifies non zero values for min and max then use them
   if (cmMin != cmMax) {
     this.cal_min = cmMin;
@@ -501,7 +1919,6 @@ NVImage.prototype.calMinMax = function () {
     this.robust_max = this.cal_max;
     return [cmMin, cmMax, cmMin, cmMax];
   }
-
   //determine full range: min..max
   let mn = this.img[0];
   let mx = this.img[0];
@@ -587,20 +2004,11 @@ NVImage.prototype.calMinMax = function () {
   } //if lo == hi
   var pct2 = this.intensityRaw2Scaled(this.hdr, lo / scl + mn);
   var pct98 = this.intensityRaw2Scaled(this.hdr, hi / scl + mn);
-  // console.log(
-  //   "full range %f..%f  (voxels 0 or NaN = %i) robust range %f..%f",
-  //   mnScale,
-  //   mxScale,
-  //   nZero,
-  //   pct2,
-  //   pct98
-  // );
   if (
     this.hdr.cal_min < this.hdr.cal_max &&
     this.hdr.cal_min >= mnScale &&
     this.hdr.cal_max <= mxScale
   ) {
-    // console.log("ignoring robust range: using header cal_min and cal_max");
     pct2 = this.hdr.cal_min;
     pct98 = this.hdr.cal_max;
   }
@@ -619,8 +2027,149 @@ NVImage.prototype.intensityRaw2Scaled = function (hdr, raw) {
   return raw * hdr.scl_slope + hdr.scl_inter;
 };
 
+function str2Buffer(str) {
+  //emulate node.js Buffer.from
+  var bytes = [];
+  for (var i = 0; i < str.length; i++) {
+    var char = str.charCodeAt(i);
+    bytes.push(char & 0xff);
+  }
+  return bytes;
+}
+
+function hdrToArrayBuffer(hdr, isDrawing8 = false) {
+  const SHORT_SIZE = 2;
+  const FLOAT32_SIZE = 4;
+
+  let byteArray = new Uint8Array(348);
+  let view = new DataView(byteArray.buffer);
+  // sizeof_hdr
+  view.setInt32(0, 348, hdr.littleEndian);
+
+  // data_type, db_name, extents, session_error, regular are not used
+
+  // dim_info
+  view.setUint8(39, hdr.dim_info);
+
+  // dims
+  for (let i = 0; i < 8; i++) {
+    view.setUint16(40 + SHORT_SIZE * i, hdr.dims[i], hdr.littleEndian);
+  }
+
+  // intent_p1, intent_p2, intent_p3
+  view.setFloat32(56, hdr.intent_p1, hdr.littleEndian);
+  view.setFloat32(60, hdr.intent_p2, hdr.littleEndian);
+  view.setFloat32(64, hdr.intent_p3, hdr.littleEndian);
+
+  // intent_code, datatype, bitpix, slice_start
+  view.setInt16(68, hdr.intent_code, hdr.littleEndian);
+  if (isDrawing8) {
+    view.setInt16(70, 2, hdr.littleEndian); //2 = DT_UNSIGNED_CHAR
+    view.setInt16(72, 8, hdr.littleEndian);
+  } else {
+    view.setInt16(70, hdr.datatypeCode, hdr.littleEndian);
+    view.setInt16(72, hdr.numBitsPerVoxel, hdr.littleEndian);
+  }
+  view.setInt16(74, hdr.slice_start, hdr.littleEndian);
+
+  // pixdim[8], vox_offset, scl_slope, scl_inter
+  for (let i = 0; i < 8; i++) {
+    view.setFloat32(76 + FLOAT32_SIZE * i, hdr.pixDims[i], hdr.littleEndian);
+  }
+  view.setFloat32(108, hdr.vox_offset, hdr.littleEndian);
+  view.setFloat32(112, hdr.scl_slope, hdr.littleEndian);
+  view.setFloat32(116, hdr.scl_inter, hdr.littleEndian);
+
+  // slice_end
+  view.setInt16(120, hdr.slice_end, hdr.littleEndian);
+
+  // slice_code, xyzt_units
+  view.setUint8(122, hdr.slice_code);
+  view.setUint8(123, hdr.xyzt_units);
+
+  // cal_max, cal_min, slice_duration, toffset
+  if (isDrawing8) {
+    view.setFloat32(124, 0, hdr.littleEndian);
+    view.setFloat32(128, 0, hdr.littleEndian);
+  } else {
+    view.setFloat32(124, hdr.cal_max, hdr.littleEndian);
+    view.setFloat32(128, hdr.cal_min, hdr.littleEndian);
+  }
+  view.setFloat32(132, hdr.slice_duration, hdr.littleEndian);
+  view.setFloat32(136, hdr.toffset, hdr.littleEndian);
+
+  // glmax, glmin are unused
+
+  // descrip and aux_file
+  //node.js byteArray.set(Buffer.from(hdr.description), 148);
+  byteArray.set(str2Buffer(hdr.description), 148);
+  //node.js: byteArray.set(Buffer.from(hdr.aux_file), 228);
+  byteArray.set(str2Buffer(hdr.aux_file), 228);
+  // qform_code, sform_code
+  view.setInt16(252, hdr.qform_code, hdr.littleEndian);
+  view.setInt16(254, hdr.sform_code, hdr.littleEndian);
+
+  // quatern_b, quatern_c, quatern_d, qoffset_x, qoffset_y, qoffset_z, srow_x[4], srow_y[4], and srow_z[4]
+  view.setFloat32(256, hdr.quatern_b, hdr.littleEndian);
+  view.setFloat32(260, hdr.quatern_c, hdr.littleEndian);
+  view.setFloat32(264, hdr.quatern_d, hdr.littleEndian);
+  view.setFloat32(268, hdr.qoffset_x, hdr.littleEndian);
+  view.setFloat32(272, hdr.qoffset_y, hdr.littleEndian);
+  view.setFloat32(276, hdr.qoffset_z, hdr.littleEndian);
+  const flattened = hdr.affine.flat();
+  // we only want the first three rows
+  for (let i = 0; i < 12; i++) {
+    view.setFloat32(280 + FLOAT32_SIZE * i, flattened[i], hdr.littleEndian);
+  }
+  //node.js https://www.w3schools.com/nodejs/met_buffer_from.asp
+  // intent_name and magic
+  //node.js byteArray.set(Buffer.from(hdr.intent_name), 328);
+  byteArray.set(str2Buffer(hdr.intent_name), 328);
+  //node.js byteArray.set(Buffer.from(hdr.magic), 344);
+  byteArray.set(str2Buffer(hdr.magic), 344);
+  return byteArray;
+  //return byteArray.buffer;
+} // hdrToArrayBuffer()
+
+NVImage.prototype.saveToDisk = async function (fnm, drawing8 = null) {
+  let isDrawing8 = !(drawing8 == null);
+  let hdrBytes = hdrToArrayBuffer(this.hdr, isDrawing8);
+  let opad = new Uint8Array(4);
+  let img8 = new Uint8Array(this.img.buffer);
+  if (isDrawing8) img8 = new Uint8Array(drawing8.buffer);
+  var odata = new Uint8Array(hdrBytes.length + opad.length + img8.length);
+  odata.set(hdrBytes);
+  odata.set(opad, hdrBytes.length);
+
+  odata.set(img8, hdrBytes.length + opad.length);
+  let saveData = null;
+  let compress = fnm.endsWith(".gz"); // true if name ends with .gz
+  if (compress) {
+    saveData = fflate.gzipSync(odata, {
+      // GZIP-specific: the filename to use when decompressed
+      filename: fnm,
+      // GZIP-specific: the modification time. Can be a Date, date string,
+      // or Unix timestamp
+      mtime: Date.now(),
+      level: 6, // the default
+    });
+  } else {
+    saveData = odata;
+  }
+  let blob = new Blob([saveData.buffer], { type: "application/octet-stream" });
+  let blobUrl = URL.createObjectURL(blob);
+  const link = document.createElement("a");
+  link.setAttribute("href", blobUrl);
+  link.setAttribute("download", fnm);
+  link.style.visibility = "hidden";
+  document.body.appendChild(link);
+  link.click();
+  document.body.removeChild(link);
+}; // saveToDisk()
+
 /**
  * factory function to load and return a new NVImage instance from a given URL
+ * @constructs NVImage
  * @param {string} url the resolvable URL pointing to a nifti image to load
  * @param {string} [name=''] a name for this image. Default is an empty string
  * @param {string} [colorMap='gray'] a color map to use. default is gray
@@ -633,34 +2182,56 @@ NVImage.prototype.intensityRaw2Scaled = function (hdr, raw) {
  * @example
  * myImage = NVImage.loadFromUrl('./someURL/image.nii.gz') // must be served from a server (local or remote)
  */
-NVImage.loadFromUrl = async function (
-  url,
+NVImage.loadFromUrl = async function ({
+  url = "",
+  urlImgData = "",
   name = "",
   colorMap = "gray",
   opacity = 1.0,
   trustCalMinMax = true,
   percentileFrac = 0.02,
   ignoreZeroVoxels = false,
-  visible = true
-) {
+  visible = true,
+} = {}) {
+  if (url === "") {
+    throw Error("url must not be empty");
+  }
   let response = await fetch(url);
-
   let nvimage = null;
-
   if (!response.ok) {
     throw Error(response.statusText);
   }
-
+  var re = /(?:\.([^.]+))?$/;
+  let ext = re.exec(url)[1];
+  if (ext.toUpperCase() === "NHDR") {
+    if (urlImgData === "") {
+    }
+  } else if (ext.toUpperCase() === "HEAD") {
+    if (urlImgData === "") {
+      urlImgData = url.substring(0, url.lastIndexOf("HEAD")) + "BRIK";
+    }
+  }
   let urlParts = url.split("/"); // split url parts at slash
   name = urlParts.slice(-1)[0]; // name will be last part of url (e.g. some/url/image.nii.gz --> image.nii.gz)
-
   let dataBuffer = await response.arrayBuffer();
+  let pairedImgData = null;
+  if (urlImgData.length > 0) {
+    let resp = await fetch(urlImgData);
+    if (resp.status === 404) {
+      if (urlImgData.lastIndexOf("BRIK") !== -1) {
+        resp = await fetch(urlImgData + ".gz");
+      }
+    }
+    pairedImgData = await resp.arrayBuffer();
+  }
+
   if (dataBuffer) {
     nvimage = new NVImage(
       dataBuffer,
       name,
       colorMap,
       opacity,
+      pairedImgData,
       trustCalMinMax,
       percentileFrac,
       ignoreZeroVoxels,
@@ -680,7 +2251,11 @@ NVImage.readFileAsync = function (file) {
     let reader = new FileReader();
 
     reader.onload = () => {
-      resolve(reader.result);
+      if (file.name.lastIndexOf("gz") !== -1) {
+        resolve(nifti.decompress(reader.result));
+      } else {
+        resolve(reader.result);
+      }
     };
 
     reader.onerror = reject;
@@ -691,6 +2266,7 @@ NVImage.readFileAsync = function (file) {
 
 /**
  * factory function to load and return a new NVImage instance from a file in the browser
+ * @constructs NVImage
  * @param {string} file the file object
  * @param {string} [name=''] a name for this image. Default is an empty string
  * @param {string} [colorMap='gray'] a color map to use. default is gray
@@ -703,24 +2279,82 @@ NVImage.readFileAsync = function (file) {
  * @example
  * myImage = NVImage.loadFromFile(SomeFileObject) // files can be from dialogs or drag and drop
  */
-NVImage.loadFromFile = async function (
-  file,
+NVImage.loadFromFile = async function ({
+  file = null, // file can be an array of file objects or a single file object
   name = "",
   colorMap = "gray",
   opacity = 1.0,
+  urlImgData = null,
   trustCalMinMax = true,
   percentileFrac = 0.02,
   ignoreZeroVoxels = false,
-  visible = true
-) {
+  visible = true,
+  isDICOMDIR = false,
+} = {}) {
   let nvimage = null;
+  let dataBuffer = [];
   try {
-    let dataBuffer = await this.readFileAsync(file);
+    if (Array.isArray(file)) {
+      for (let i = 0; i < file.length; i++) {
+        dataBuffer.push(await this.readFileAsync(file[i]));
+      }
+    } else {
+      dataBuffer = await this.readFileAsync(file);
+    }
+    let pairedImgData = null;
+    if (urlImgData) {
+      pairedImgData = await this.readFileAsync(urlImgData);
+    }
+    name = file.name;
     nvimage = new NVImage(
       dataBuffer,
       name,
       colorMap,
       opacity,
+      pairedImgData,
+      trustCalMinMax,
+      percentileFrac,
+      ignoreZeroVoxels,
+      visible,
+      isDICOMDIR
+    );
+  } catch (err) {
+    log.debug(err);
+  }
+  return nvimage;
+};
+
+NVImage.loadFromBase64 = async function ({
+  base64 = null,
+  name = "",
+  colorMap = "gray",
+  opacity = 1.0,
+  trustCalMinMax = true,
+  percentileFrac = 0.02,
+  ignoreZeroVoxels = false,
+  visible = true,
+} = {}) {
+  //https://stackoverflow.com/questions/21797299/convert-base64-string-to-arraybuffer
+  function base64ToArrayBuffer(base64) {
+    var binary_string = window.atob(base64);
+    var len = binary_string.length;
+    var bytes = new Uint8Array(len);
+    for (var i = 0; i < len; i++) {
+      bytes[i] = binary_string.charCodeAt(i);
+    }
+    return bytes.buffer;
+  }
+
+  let nvimage = null;
+  try {
+    let dataBuffer = base64ToArrayBuffer(base64);
+    let pairedImgData = null;
+    nvimage = new NVImage(
+      dataBuffer,
+      name,
+      colorMap,
+      opacity,
+      pairedImgData,
       trustCalMinMax,
       percentileFrac,
       ignoreZeroVoxels,
@@ -761,8 +2395,8 @@ NVImage.prototype.zeroImage = function () {
 
 /**
  * Image M.
- * @typedef {Object} NVImage~MetaData
- * @property {uuidv4} id - unique if of image
+ * @typedef {Object} NVImageMetadata
+ * @property {string} id - unique if of image
  * @property {number} datatypeCode - data type
  * @property {number} nx - number of columns
  * @property {number} ny - number of rows
@@ -777,7 +2411,7 @@ NVImage.prototype.zeroImage = function () {
 
 /**
  * get nifti specific metadata about the image
- * @returns {NVImage~Metadata} - {@link NVImage~Metadata}
+ * @returns {NVImageMetadata} - {@link NVImageMetadata}
  */
 NVImage.prototype.getImageMetadata = function () {
   const id = this.id;
@@ -811,18 +2445,27 @@ NVImage.prototype.getImageMetadata = function () {
 /**
  * a factory function to make a zero filled image given a NVImage as a reference
  * @param {NVImage} nvImage an existing NVImage as a reference
+ * @param {dataType} string the output data type. Options: 'same', 'uint8'
  * @returns {NVImage} returns a new NVImage filled with zeros for the image data
  * @example
  * myImage = NVImage.loadFromFile(SomeFileObject) // files can be from dialogs or drag and drop
  * newZeroImage = NVImage.zerosLike(myImage)
  */
-NVImage.zerosLike = function (nvImage) {
+NVImage.zerosLike = function (nvImage, dataType = "same") {
+  // dataType can be: 'same', 'uint8'
+  // 'same' means that the zeroed image data type is the same as the input image
   let zeroClone = nvImage.clone();
   zeroClone.zeroImage();
+  if (dataType === "uint8") {
+    zeroClone.img = Uint8Array.from(zeroClone.img);
+    zeroClone.hdr.datatypeCode = zeroClone.DT_UNSIGNED_CHAR;
+    zeroClone.hdr.numBitsPerVoxel = 8;
+  }
   return zeroClone;
 };
 
 String.prototype.getBytes = function () {
+  //CR??? What does this do?
   let bytes = [];
   for (var i = 0; i < this.length; i++) {
     bytes.push(this.charCodeAt(i));
@@ -865,28 +2508,28 @@ NVImage.prototype.getValue = function (x, y, z) {
  */
 function getExtents(positions, forceOriginInVolume = true) {
   let nV = (positions.length / 3).toFixed(); //each vertex has 3 components: XYZ
-  let origin = mat.vec3.fromValues(0, 0, 0); //default center of rotation
-  let mn = mat.vec3.create();
-  let mx = mat.vec3.create();
+  let origin = vec3.fromValues(0, 0, 0); //default center of rotation
+  let mn = vec3.create();
+  let mx = vec3.create();
   let mxDx = 0.0;
   let nLoops = 1;
   if (forceOriginInVolume) nLoops = 2; //second pass to reposition origin
   for (let loop = 0; loop < nLoops; loop++) {
     mxDx = 0.0;
     for (let i = 0; i < nV; i++) {
-      let v = mat.vec3.fromValues(
+      let v = vec3.fromValues(
         positions[i * 3],
         positions[i * 3 + 1],
         positions[i * 3 + 2]
       );
       if (i === 0) {
-        mat.vec3.copy(mn, v);
-        mat.vec3.copy(mx, v);
+        vec3.copy(mn, v);
+        vec3.copy(mx, v);
       }
-      mat.vec3.min(mn, mn, v);
-      mat.vec3.max(mx, mx, v);
-      mat.vec3.subtract(v, v, origin);
-      let dx = mat.vec3.len(v);
+      vec3.min(mn, mn, v);
+      vec3.max(mx, mx, v);
+      vec3.subtract(v, v, origin);
+      let dx = vec3.len(v);
       mxDx = Math.max(mxDx, dx);
     }
     if (loop + 1 >= nLoops) break;
@@ -896,7 +2539,7 @@ function getExtents(positions, forceOriginInVolume = true) {
       if (mx[j] < origin[j]) ok = false;
     }
     if (ok) break;
-    mat.vec3.lerp(origin, mn, mx, 0.5);
+    vec3.lerp(origin, mn, mx, 0.5);
     log.debug("origin moved inside volume: ", origin);
   }
   let min = [mn[0], mn[1], mn[2]];
@@ -943,44 +2586,29 @@ NVImage.prototype.toNiivueObject3D = function (id, gl) {
     this.matRAS
   );
 
-  const positions = [
+  let posTex = [
+    //spatial position (XYZ), texture coordinates UVW
     // Superior face
     ...LPS,
+    ...[0.0, 0.0, 1.0],
     ...RPS,
+    ...[1.0, 0.0, 1.0],
     ...RAS,
+    ...[1.0, 1.0, 1.0],
     ...LAS,
+    ...[0.0, 1.0, 1.0],
 
     // Inferior face
     ...LPI,
+    ...[0.0, 0.0, 0.0],
     ...LAI,
+    ...[0.0, 1.0, 0.0],
     ...RAI,
+    ...[1.0, 1.0, 0.0],
     ...RPI,
+    ...[1.0, 0.0, 0.0],
   ];
 
-  const textureCoordinates = [
-    // Superior Z=1.0
-    0.0, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 1.0, 1.0,
-
-    // Inferior Z=1.0
-    0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0, 1.0, 0.0, 0.0,
-
-    // Anterior Y=1
-    0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.0,
-
-    // Posterior Y=0
-    0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 1.0,
-
-    // Right X=1
-    1.0, 0.0, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 1.0,
-
-    // Left X=0
-    0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0, 1.0, 0.0,
-  ];
-
-  const vertexBuffer = gl.createBuffer();
-  gl.bindBuffer(gl.ARRAY_BUFFER, vertexBuffer);
-  gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(positions), gl.STATIC_DRAW);
-
   const indexBuffer = gl.createBuffer();
   gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, indexBuffer);
 
@@ -989,6 +2617,7 @@ NVImage.prototype.toNiivueObject3D = function (id, gl) {
   // position.
 
   const indices = [
+    //six faces of cube: each has 2 triangles (6 indices)
     0,
     3,
     2,
@@ -1034,28 +2663,45 @@ NVImage.prototype.toNiivueObject3D = function (id, gl) {
     gl.STATIC_DRAW
   );
 
-  const textureCoordBuffer = gl.createBuffer();
-  gl.bindBuffer(gl.ARRAY_BUFFER, textureCoordBuffer);
-  gl.bufferData(
-    gl.ARRAY_BUFFER,
-    new Float32Array(textureCoordinates),
-    gl.STATIC_DRAW
-  );
+  const posTexBuffer = gl.createBuffer();
+  gl.bindBuffer(gl.ARRAY_BUFFER, posTexBuffer);
+  gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(posTex), gl.STATIC_DRAW);
+
+  const vao = gl.createVertexArray();
+  gl.bindVertexArray(vao);
+  gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, indexBuffer);
+  gl.bindBuffer(gl.ARRAY_BUFFER, posTexBuffer);
+  //vertex spatial position: 3 floats X,Y,Z
+  gl.enableVertexAttribArray(0);
+  gl.vertexAttribPointer(0, 3, gl.FLOAT, false, 24, 0);
+  //UVW texCoord: (also three floats)
+  gl.enableVertexAttribArray(1);
+  gl.vertexAttribPointer(1, 3, gl.FLOAT, false, 24, 12);
+  gl.bindVertexArray(null);
 
   const obj3D = new NiivueObject3D(
     id,
-    vertexBuffer,
+    posTexBuffer,
     gl.TRIANGLES,
     indices.length,
     indexBuffer,
-    textureCoordBuffer
+    vao
   );
 
-  const extents = getExtents(positions);
+  const extents = getExtents([
+    ...LPS,
+    ...RPS,
+    ...RAS,
+    ...LAS,
+    ...LPI,
+    ...LAI,
+    ...RAI,
+    ...RPI,
+  ]);
   obj3D.extentsMin = extents.min;
   obj3D.extentsMax = extents.max;
   obj3D.furthestVertexFromOrigin = extents.furthestVertexFromOrigin;
-  obj3D.originNegate = mat.vec3.clone(extents.origin);
-  mat.vec3.negate(obj3D.originNegate, obj3D.originNegate);
+  obj3D.originNegate = vec3.clone(extents.origin);
+  vec3.negate(obj3D.originNegate, obj3D.originNegate);
   return obj3D;
 };