How can I ignore files/subjects with error?

[Sangwook]

Hi,

I tried using med-imagetools to process the dataset.

But I got an error and it stopped. Is there any way to ignore the files with an error and make it keep processing?

Just in case the error message is:

Traceback (most recent call last):
  File "/cluster/home/kimsa/anaconda3/envs/torch38/lib/python3.8/site-packages/imgtools/modules/structureset.py", line 114, in get_mask
    mask[z, :, :, idx] += slice_mask
IndexError: index 119 is out of bounds for axis 0 with size 119

Thank you!

[Sejin Kim]

it seems like the image-mask geometry is slightly offset and the slice you're looking to add is just outside of the size of the image.
try using the --warn_on_error flag to skip bad samples.

[Sangwook]

Thank you! I will try using the flag :)

[Sangwook]

It works! Thank you @skim2257 :)