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[rodrigobasilio2022]

@thewtex @glehmann

I am receiving these outputs when trying to register two volumes in the browser using the wasm package

My bets are in the memory usage. I think it needs more than 4GB

The size of the volumes are 512x512x328 and 512x512x333

Is there a way to overcome this problem?

[thewtex]

Hi @rodrigobasilio2022 ,

I am working on a solution to progressively register across scales and chunks that will limit memory usage and improve speed.

I the meantime, you could use @itk-wasm/downsample, register downsampled images, then apply the transformation to the full resolution input.

[rodrigobasilio2022]

Is there an example somewhere in how to do that? The Elastix didn't seem to have a apply only command

[thewtex]

👍 I'll create an example.

[rodrigobasilio2022]

Actually I just need the last part. There isn't transformix for typescript

[rodrigobasilio2022]

Dont know if it is related but this are happening when I try to coregister two volumes of 512x512x163

[rodrigobasilio2022]

@thewtex Here is a snippet code. If you can point me out what I should do it will be nice...

export async function downSampleImage(
  image,
  name: string,
  shrinkFactors = [4, 4, 4]
): Promise<Image> {
  const { downsampled: imageDownsampled } = await downsampleBinShrink(image, {
    shrinkFactors,
  });
  imageDownsampled.name = name;
  return imageDownsampled;
}

export async function automaticCoregistration(
  fixedImageData: vtkImageData,
  movingImageData: vtkImageData,
  parameterMap: JsonCompatible
) {
  return new Promise(async (resolve, reject) => {
    try {
      console.log('Starting automatic co-registration with parameters:', parameterMap);

      // Convert vtkImageData to ITK images
      const fixedImage = getImageFromImageData(fixedImageData, 'fixed');
      const movingImage = getImageFromImageData(movingImageData, 'moving');

      // Validate images
      if (!fixedImage || !movingImage) {
        throw new Error('Failed to convert image data. Make sure both volumes are valid.');
      }

      if (!fixedImage.data || !movingImage.data) {
        throw new Error('Image data is missing. Cannot proceed with registration.');
      }

      console.log('Fixed image size:', fixedImage.size);
      console.log('Moving image size:', movingImage.size);
      console.log('Fixed image data length:', fixedImage.data.length);
      console.log('Moving image data length:', movingImage.data.length);

      // Create elastix options
      let elastixOptions: ElastixOptions;

      const startTime = performance.now();
      console.log('Starting elastix registration...');

      const downSampleImages = true; // Set to true to downsample images
      if (downSampleImages) {
        const fixedDownSampled = await downSampleImage(fixedImage, 'fixed');
        const movingDownSampled = await downSampleImage(movingImage, 'moving');
	    elastixOptions = {
           fixed: fixedDownSampled,
           moving: movingDownSampled,
           initialTransform: undefined,
           initialTransformParameterObject: undefined,
        };
		
      } else {
	    elastixOptions = {
           fixed: fixedImage,
           moving: movingImage,
           initialTransform: undefined,
           initialTransformParameterObject: undefined,
        };
	  }
      // Run elastix registration
      let elastixResult = await elastix([parameterMap], 'transform.h5', elastixOptions);

      const totalTime = performance.now() - startTime;
      const { transformParameterObject } = elastixResult;
      if (downSampleImages) {
        parameterMap['MaximumNumberOfIterations'] = ['0'];
        elastixResult = await elastix([parameterMap], 'finalTransform', {
          fixed: fixedImage,
          moving: movingImage,
          initialTransformParameterObject: transformParameterObject, // use the transform from step 2
        });
      }

      console.log('Elastix registration completed in', totalTime, 'ms');
      console.log('Transform parameter object:', transformParameterObject);

      resolve(elastixResult);
    } catch (error: any) {
      console.error('Error in automatic co-registration:', error);
      reject('Error in automatic co-registration: ${error.message}');
    }
  });
}

The second elastix appears to perform all the steps again, not just apply the final transformation.

[thewtex]

@rodrigobasilio2022 thanks, I am working on a PR

[thewtex]

@rodrigobasilio2022 example:

4370ecc

[rodrigobasilio2022]

@thewtex. Many thanks for the response

Need to wait for the merge right?
I tested with these two files and it didnt work well. The files were already downsampled using [4, 4, 4]
The pipeline works with volumes it already works, but not with these and there is no error message to help unbderstand what is happening

moving-elastix.nii.gz
fixed-elastix.nii.gz

[thewtex]

Hi @rodrigobasilio2022 , no the package has been pushed to NPM.

For that particular example, we need to add:

rigidParameterMap.CheckNumberOfSamples = ["false"];

To the parameters.

Here's the full script:

https://github.com/thewtex/itk-elastix-wasm-ct-head-torso-example

[rodrigobasilio2022]

@thewtex Again many thanks for your response. This parameter only works in rigid transform or we can use in other transformation types? In an combined transformation setup only the first need it or all transforms need it?

[thewtex]

@rodrigobasilio2022 other transformation types should work, too. For this data, where we are aligning a small portion of the head to the torso, disabling CheckNumberOfSamples on the parameters is helpful.