[ITK] Tests with multi-file input data (Bruker2DSEQ)

[Wood, Tobias]

Thanks very much Brad. Individual responses below.

> If you need an entire folder, you can create it here. I am not sure what problem you encountered with this layout.

To be honest, I didn’t try it. I assumed it would cause problems. I will try it.

> There are quite a number of options for referencing files series, file pair, and associated directories. I would expect this to meet you needs.

Again thanks - I had completely missed this documentation.

> It’s not clear to me what files are needed when reading, if you need recommendation on using `DATA{}` please be specific with the files needed by the IO, and their locations.

The bare minimum required to read the image are the ‘2dseq’ and ‘visu_pars’ file. I have kept the convention of the old Bruker reader which is to specify the ‘2dseq’ file as the input, and then to work out the paths to ‘visu_pars’ and the other headers.

The Bruker format is a bit complex. The issue is that each acquisition can be reconstructed multiple times. The directory structure goes something like this:

acquistion/
	method	<- An important header file
	acqp		<- Another important header
	fid		<- Raw data
	***bunch of other stuff***
	pdata/
		1/
			2dseq		<- Reconstructed data
      		visu_pars	<- Most important header
      		reco		<- Less important header, mostly duplicated in visu_pars
			procs		<- Unimportant header
			id		<- Unimportant header
		2/
      		2dseq
			visu_pars
			reco
      		procs
			id
		...

I hope the indentation survives transmission. Here, 1 and 2 are different reconstructed images, for instance magnitude and phase, or for diffusion it might be raw images and a multi-volume file containing FA, MD etc. as calculated by ParaVision.

From Paravision 6 onwards, the bare minimum to read an image seems to be 2dseq + visu_pars. However, some important meta-data like diffusion b-values and b-vectors is only present in the method header. Hence I’m not entirely sure what should be considered a valid “image” by ITK - just 2dseq + visu_pars, or the entire data structure?

For my uses, I think the best approach would be to consider 2dseq + visu_pars the minimum, but if the other headers are present read them in to get the meta-data. Is that acceptable?

Best wishes,
Toby