wazeerzulfikar / mri-deface-detector Goto Github PK

When trying to load this file https://openneuro.org/datasets/ds000114/versions/1.0.0/file-display/sub-01:ses-retest:anat:sub-01_ses-retest_T1w.nii.gz

Uncaught (in promise) Error: total size of new array must be unchanged
    at new ValueError (bundle.js:109527)
    at NdArray.reshape (bundle.js:111220)
    at preprocess (bundle.js:112)
    at FileReader.reader.onload (bundle.js:90)

Create a single figure with an example of: (a) original undefaced image (b) defaced image (c) downsampled original (d) downsampled defaced (e) mean of downsampled original (f) mean of downsampled defaced.

This could go into README or somewhere else.

The ability to run this from the web is very useful.

This tool makes a strong assumption that the input image is in RAS orientation. Consider the sagittal T1 scan from this public dataset. Since this was a 3D acquisition, dcm2niix can losslessly rotate the image to RAS orientation or preserve the original sagittal alignment (PSR orientation) depending on the -x flag:

 dcm2niix -f PSR -x i ~/dicom/path/T1
 dcm2niix -f RAS -xy ~/dicom/path/T1

Even though the image data is identical (just with the dimensions swizzled), this detector fails for the PSR image.

Note that dcm2niix will only re-orient 3D acquisitions (to preserve slice timing of 2D sequences). Note that some T1 anatomical scans are 2D.

When loading https://wazeerzulfikar.github.io/Deface-Detector/ (prior to even selecting input file)

Uncaught Error: Node's Buffer() not available
    at Object.<anonymous> (bundle.js:36852)
    at Object.244.buffer (bundle.js:36928)
    at o (bundle.js:1)
    at bundle.js:1
    at Object.1.@tensorflow/tfjs (bundle.js:5)
    at o (bundle.js:1)
    at r (bundle.js:1)
    at bundle.js:1

This will increase reproducibility and allow others to contribute to the project.

1. Install npm
2. Navigate to directory with package.json
3. Missing numjs dependency (error below)
   Error: Cannot find module 'numjs' from 'C:\Users\adoyle\PycharmProjects\Deface-Detector'
4. Missing model file (error below)
   Error: Cannot find module './public/data/mri_full_uint8.json' from 'C:\Users\adoyle\PycharmProjects\Deface-Detector'