rcuocolo
commented
2 years ago Thank you for signaling the problem. I am out of office but will look into it when I come back to work. I did run a script to clean up this issue in the past, so it is somewhat surprising. It used FSL functions to identify clusters and remove small ones, as misclicks can happen in a manual segmentation process. If you have fixed masks as well (i.e., have already ran a script to remove inappropriate clusters), feel free to make a request to substitute the problematic files with the correct ones, as it would speed up the process.
Il Gio 7 Lug 2022, 11:28 meglaficus @.***> ha scritto:
Hi, we are working working with your label set and I have come across some errors in the zonal masks. Here is a list of whole prostate masks with more than one connected component:
ProstateX-0000.nii.gz has 3 ccs ProstateX-0014.nii.gz has 2 ccs ProstateX-0027.nii.gz has 2 ccs ProstateX-0064.nii.gz has 25 ccs ProstateX-0112.nii.gz has 2 ccs ProstateX-0126.nii.gz has 2 ccs ProstateX-0141.nii.gz has 2 ccs ProstateX-0142.nii.gz has 2 ccs ProstateX-0168.nii.gz has 5 ccs ProstateX-0170.nii.gz has 2 ccs ProstateX-0172.nii.gz has 2 ccs ProstateX-0174.nii.gz has 2 ccs ProstateX-0179.nii.gz has 2 ccs ProstateX-0181.nii.gz has 2 ccs ProstateX-0182.nii.gz has 4 ccs ProstateX-0183.nii.gz has 5 ccs ProstateX-0190.nii.gz has 3 ccs ProstateX-0194.nii.gz has 2 ccs ProstateX-0198.nii.gz has 4 ccs ProstateX-0203.nii.gz has 3 ccs ProstateX-087.nii.gz has 8 ccs
Most of these have similar errors in the seperate peripheral and non-peripheral zone masks. I have merged the peripheral and non-peripheral masks for each patient and here are the cases where these errors persist:
ProstateX-0000.nii.gz has 3 ccs ProstateX-0014.nii.gz has 2 ccs ProstateX-0027.nii.gz has 2 ccs ProstateX-0064.nii.gz has 25 ccs ProstateX-0087.nii.gz has 8 ccs ProstateX-0112.nii.gz has 2 ccs ProstateX-0168.nii.gz has 2 ccs ProstateX-0170.nii.gz has 2 ccs ProstateX-0172.nii.gz has 2 ccs ProstateX-0179.nii.gz has 2 ccs ProstateX-0183.nii.gz has 3 ccs
The errors range from small, single voxel abrations close to the actual mask to larger errors that are very far from the mask and have a large impact on distance-based metrics.
Thank you for an otherwise terrific dataset, Jakob
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meglaficus
Hi, we are working working with your label set and I have come across some errors in the zonal masks. Here is a list of whole prostate masks with more than one connected component:
ProstateX-0000.nii.gz has 3 ccs ProstateX-0014.nii.gz has 2 ccs ProstateX-0027.nii.gz has 2 ccs ProstateX-0064.nii.gz has 25 ccs ProstateX-0112.nii.gz has 2 ccs ProstateX-0126.nii.gz has 2 ccs ProstateX-0141.nii.gz has 2 ccs ProstateX-0142.nii.gz has 2 ccs ProstateX-0168.nii.gz has 5 ccs ProstateX-0170.nii.gz has 2 ccs ProstateX-0172.nii.gz has 2 ccs ProstateX-0174.nii.gz has 2 ccs ProstateX-0179.nii.gz has 2 ccs ProstateX-0181.nii.gz has 2 ccs ProstateX-0182.nii.gz has 4 ccs ProstateX-0183.nii.gz has 5 ccs ProstateX-0190.nii.gz has 3 ccs ProstateX-0194.nii.gz has 2 ccs ProstateX-0198.nii.gz has 4 ccs ProstateX-0203.nii.gz has 3 ccs ProstateX-087.nii.gz has 8 ccs
Most of these have similar errors in the seperate peripheral and non-peripheral zone masks. I have merged the peripheral and non-peripheral masks for each patient and here are the cases where these errors persist:
ProstateX-0000.nii.gz has 3 ccs ProstateX-0014.nii.gz has 2 ccs ProstateX-0027.nii.gz has 2 ccs ProstateX-0064.nii.gz has 25 ccs ProstateX-0087.nii.gz has 8 ccs ProstateX-0112.nii.gz has 2 ccs ProstateX-0168.nii.gz has 2 ccs ProstateX-0170.nii.gz has 2 ccs ProstateX-0172.nii.gz has 2 ccs ProstateX-0179.nii.gz has 2 ccs ProstateX-0183.nii.gz has 3 ccs
The errors range from small, single voxel abrations close to the actual mask to larger errors that are very far from the mask and have a large impact on distance-based metrics.
Thank you for an otherwise terrific dataset, Jakob