Issues with translation of images

[KevinAquino]

First off - great tool!

I am having trouble with the tool, in ITK-snap and the imported DICOM the centres in the axial plane are way off (see below)

I am looking at the dataset:
https://openneuro.org/datasets/ds003949/versions/1.0.1

specifically in that example sub-336, I can't seem to find the error. I assume it's something to do with the way that the slice positions are calculated.

Any help would be great!

[KevinAquino]

I guess also that its a sagittal acquisition, that might change things?

I think that would the issue - usually in these open datasets there is an accompanying json - could you use that to help out the reconstruction?

[tomaroberts]

@KevinAquino – thanks for raising this issue. Sorry for slow reply, was away last week.

Let me look into this and I'll get back to you with a fix or some thoughts.

[KevinAquino]

Great thank you!

[tomaroberts]

@KevinAquino – I've started looking into this, but I need more time to dig into it.

A couple of questions for you:

1. Have you observed any rotational issues across the datasets you've been using nii2dcm? Or just translational issues?

2. In your original screenshot, how did you bring up the offset origin crosshair in the right hand image? I'm not sure how to do that in ITK-Snap as I usually use MITKWorkbench for 3D work like this, but it would good to make the same comparison that you are in ITK-Snap as different software can interpret DICOM metadata differently. Thanks.