Nick Tustison
Nick Tustison
If you were so inclined, that would be a much appreciated contribution.
For starters, the second argument should only have 3 elements (instead of 4).
What program are you using to visualize your results?
My guess is it's an issue related to package differences ([e.g., nifty header](https://github.com/ANTsX/ANTs/wiki/How-does-ANTs-handle-qform-and-sform-in-NIFTI-1-images%3F)). As a result, visualizations can vary. If you want me to take a closer look, you'll need...
Yeah, it's a nifti header issue, as mentioned above. If you open the image in ITK-SNAP, they're both consistently displayed (see below). As explained in the Wiki page, other packages,...
This is what I get when I resample and view the results within ANTs/ITK: ``` >>> import ants >>> t2_ants = ants.image_read("3D_FLAIR.nii") >>> t2_ants_resampled = ants.resample_image(t2_ants, (0.67, 0.67, 5.5), use_voxels=False,...
Note that this is a much more general problem beyond ANTs that involves multiple neuroimaging packages. For example, see the discussion [here](https://discourse.itk.org/t/saving-non-orthogonal-volume-in-nifti-format/2760/11).
The underlying joint label fusion process requires more than 1 atlas and the specific task is for 6-tissue labeling (CSF, GM, WM, Deep GM, brain stem and cerebellum). Here are...
All the options for the script are meant strictly for producing the cortical thickness images. The issue of how one parcellates those thickness images, e.g., Hammersmith Atlas, is completely outside...
Yes, try that.