I am currently using the Deep-Atlas full-pipeline to download and warp some gene datasets into the CCF volume.
I have a common issue from ITK for specific datasets: 67979023, 67979024, 67979025, 67979026, 67979027
The error is:
ITK ERROR: Total Mass of the image was zero. Aborting here to prevent division by zero later on.
Basically, the gene dataset is downloaded, but the registration turned into this error.
I already faced this kind of error on ITK when some slices only have zero values in it, especially using the Mutual Information from the SyN mode. I solved it by checking if the considered slice does not only have zero values to know whether on not to launch the registration.
But in this case actually, I watched the downloaded slices and no one seemed to be empty.
Here is the command I launched for the first dataset:
Singularity> python proj62/piluso/deep-atlas/full_pipeline.py --coordinate-sys ccfv2 --downsample-img 2 --interpolator-name rife --interpolator-checkpoint proj62/piluso/deep-atlas/interpolation/interpolation-checkpoints/rife/ proj62/piluso/deep-atlas/data/ara_nissl_25.nrrd proj62/piluso/deep-atlas/data/annotations_25_ccfv2.nrrd proj62/piluso/deep-atlas/data/annotation_25_ccfv3.nrrd 67979023 proj62/piluso/tmp
Unfortunately I don't know how to solve this issue... Thanks for helping!
I am currently using the Deep-Atlas full-pipeline to download and warp some gene datasets into the CCF volume. I have a common issue from ITK for specific datasets: 67979023, 67979024, 67979025, 67979026, 67979027
The error is:
ITK ERROR: Total Mass of the image was zero. Aborting here to prevent division by zero later on.Basically, the gene dataset is downloaded, but the registration turned into this error.I already faced this kind of error on ITK when some slices only have zero values in it, especially using the Mutual Information from the SyN mode. I solved it by checking if the considered slice does not only have zero values to know whether on not to launch the registration. But in this case actually, I watched the downloaded slices and no one seemed to be empty.
Here is the command I launched for the first dataset:
Singularity> python proj62/piluso/deep-atlas/full_pipeline.py --coordinate-sys ccfv2 --downsample-img 2 --interpolator-name rife --interpolator-checkpoint proj62/piluso/deep-atlas/interpolation/interpolation-checkpoints/rife/ proj62/piluso/deep-atlas/data/ara_nissl_25.nrrd proj62/piluso/deep-atlas/data/annotations_25_ccfv2.nrrd proj62/piluso/deep-atlas/data/annotation_25_ccfv3.nrrd 67979023 proj62/piluso/tmpUnfortunately I don't know how to solve this issue... Thanks for helping!