chp_mask.nii.gz file error

[Luoyu-Wang]

Hi! We have used version 1.0.1 of the Docker to process T1 images and have generated a chp_mask.nii.gz file. However, we are unable to open or view this file with tools like MRICron, SPM, etc. This issue did not occur with version 1.0.0, where everything worked fine.

Could you please provide guidance or a solution for this problem?

[CenterImagingBiomarkerDevelopment]

Hello Luoyu-Wang,

You should be able to load the segmentation map on any MRI visualization software. I tested it using ItkSNAP, FSLeyes, MRICron, and Slicer.

However, with the new update of the software, the first step involving rigid registration had sub-optimal parameters leading to the misalignment of the image. This could explain why you had an empty segmentation mask.

Can you try to re-download the docker? docker pull kilianhett/chp_seg:1.0.1 and try it again.

Please let me know if it solves your problem.

Best, Kilian

[Luoyu-Wang]

Hi, Here is my data and segmentation. We update the images but it appears that the errors still persist.

n4oS0001.nii.gz n4oS0001_chp_mask.nii.gz Here is a screenshot of the error report error.zip

[CenterImagingBiomarkerDevelopment]

Thank you for sharing your files with me.

I was able to open them using itksnap (see screenshot). I believe the issue comes from the format of voxel, here in long integer, which seems incompatible with your system (but also sub-optimal for storage purposes). I pushed a correction that fixed it, the values are now encoded on 8 bits as unsigned integers.

Could you please re-download the last version of the docker? ("docker pull kilianhett/chp_seg:1.0.1")

[Luoyu-Wang]

Thank you for your help, and the problem has been solved.