Closed GerardMJuan closed 11 months ago
Hi @GerardMJuan, it seems to be a problem related to the affine matrix in nii file. Could share me with one stack of your data to test? If you are not able to share the data, could you share with me the affine matrix as follows?
import nibabel as nib
img = nib.load(file_path)
print(img.header["pixdim"][1:4])
print(img.affine)
print(img.get_qform())
print(img.get_sform())
Hi,
I am not able to share the data, and did not find any issues with the affine matrix. However, I just tried it now with same command, same image, same data and it seems to work now. The most plausible explanation for this change, I believe, is that I was running it on a HPC environment and the GPU/node I was selecting last week had some type of weird incompatibility, and the one I am selecting now is not.
Anyway, now it works perfectly well. Sorry for bothering you. Closing this issue. If in the future I am able to reproduce it and have more information I will let you know.
Best, Gerard
I have an issue when using
nesvor segment-stack
. It fails, giving a SVD error when trying to save the . I have tried with different images, so it is not related to the input. I am using the docker image, version 0.5.0. I have also tried it in a HPC environment (converting the image to a singularity container), getting the same error.This is the full error stack:
Note that the rest of the tool works great: when using Monaifbs separately and providing NeSVoR with the masks, everything works smoothly. So a workaround right now is to compute the masks outside of the docker.
It is not a memory issue, and I have manually checked the images and they have no issues (Monaifbs works well with the same images when used in my own installation).