I have tried to submit my hippocampus segmentation masks, but I get an error in the log file: RuntimeError: Exception thrown in SimpleITK Image_CopyInformation: /tmp/SimpleITK/Code/Common/src/sitkImage.cxx:352: sitk::ERROR: Source image size of [ 195, 233, 159 ] does not match this image's size of [ 197, 233, 189 ]! I have ensured that the shape of my segmentation masks match the shape of the 12 validation images i found (some being 195, 233, 159, others 197, 233, 18. Did I segment the wrong images? I downloaded and ran inference on the 12 that are found in Task 2 - Segmentation Validation. I made sure to do them in order. Can anyone help?
Created by Abel Koffeman JustBeSimple I have already submitted the validation phase result on time. For the test phase, I was trying to check the output images as I made some changes in the pipeline. I don't think you can make any more submissions to the validation pool as the time window is closed. As far I am concern the validaton phase ends. If i submit results again in the validation environment, will it be any issue? Hi @JustBeSimple,
I had also seen the same error initially. The files are getting matched incorrectly because of naming of the segmentation prediction,
I think there is a mistake in the submission guide. The prediction files should be named as LISAHF1234segprediction.nii.gz with only '4' digit ID as per the original format. The guide erroneously indicates it as 5 digit ID.
Hope this helps.
Regards,
Sharat Hi @JustBeSimple,
Please follow the instructions here: https://www.synapse.org/Synapse:syn65670170/wiki/631805 and ensure that your output files are named correctly. Otherwise, your submission will be considered invalid.
Thanks,
The LISA 2025 Challenge Organizers I made sure they align and wrote a script to check this:
Mask File Mask Shape Image File Image Shape
--------------------------------------------------------------------------------------------------------------
LISA_HF_00001_seg_prediction.nii.gz (195, 233, 159) LISA_VALIDATION_0001_ciso.nii.gz (195, 233, 159)
LISA_HF_00002_seg_prediction.nii.gz (195, 233, 159) LISA_VALIDATION_0002_ciso.nii.gz (195, 233, 159)
LISA_HF_00003_seg_prediction.nii.gz (195, 233, 159) LISA_VALIDATION_0003_ciso.nii.gz (195, 233, 159)
LISA_HF_00004_seg_prediction.nii.gz (197, 233, 189) LISA_VALIDATION_0004_ciso.nii.gz (197, 233, 189)
LISA_HF_00005_seg_prediction.nii.gz (195, 233, 159) LISA_VALIDATION_0005_ciso.nii.gz (195, 233, 159)
LISA_HF_00006_seg_prediction.nii.gz (195, 233, 159) LISA_VALIDATION_0006_ciso.nii.gz (195, 233, 159)
LISA_HF_00007_seg_prediction.nii.gz (195, 233, 159) LISA_VALIDATION_0007_ciso.nii.gz (195, 233, 159)
LISA_HF_00008_seg_prediction.nii.gz (197, 233, 189) LISA_VALIDATION_0008_ciso.nii.gz (197, 233, 189)
LISA_HF_00009_seg_prediction.nii.gz (195, 233, 159) LISA_VALIDATION_0009_ciso.nii.gz (195, 233, 159)
LISA_HF_00010_seg_prediction.nii.gz (197, 233, 189) LISA_VALIDATION_0010_ciso.nii.gz (197, 233, 189)
LISA_HF_00011_seg_prediction.nii.gz (197, 233, 189) LISA_VALIDATION_0011_ciso.nii.gz (197, 233, 189)
LISA_HF_00012_seg_prediction.nii.gz (197, 233, 189) LISA_VALIDATION_0012_ciso.nii.gz (197, 233, 189)
and i still run into the same error: sitk::ERROR: Source image size of [ 195, 233, 159 ] does not match this image's size of [ 197, 233, 189 ]!
Hi @JustBeSimple,
The validation set contains images of different shapes (some are 195×233×159, others 197×233×189). You’ll need to make sure your masks match the exact shape of the corresponding case before submission.
Best,
The LISA 2025 Challenge Organizers