Total segmentation volume is too small. Segmentation may be corrupted. #256
Comments
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Thanks for reporting. Indeed the segmentation looks ok ( on my phone). What volume number are you getting? Maybe our threshold is too conservative. |
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This is the |
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Thanks, the volume is 0.77 liter which is also our threshold , in our tests we did not encounter such small volumes except if the segmentation was broken. In your case the segmentation looks good, so the threshold can be decreased. FastSurfer/FastSurferCNN/quick_qc.py Line 47 in 617ed0d I reduced it in dev to 0.75 , so one option is to checkout dev and build a docker/singularity image from that (note that there are some other commits in dev and it has not been thoroughly tested), or create a new image from your stable image after entering the image and manually changing that value in quick_qc.py . I wish we had a flag to ignore those errors, but currently we don't. |
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Thanks for the quick edit. If my call is exactly that and that's all I'm planning at the moment, is there anything in the |
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I think you should just be able to run no dev or modifications needed, just use stable / your existing image. |
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I'll give it a shot and see if it work. Thanks. |
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Using |
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Just another use case in this dataset. This individual has a total volume of 0.72.
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Are these adults? I guess we need to go even lower or switch off the test and come up with something different. |
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Just switched from ERROR to a WARNING in dev. You can checkout stable, copy quick_qc.py over from dev and re-build the containers. We may also push a hot fix release at some point. |
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I created a stable patch release v2.0.2 that gives a WARNING and continues. We will probably update docker images today or tomorrow. In the future we need to:
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Thanks @m-reuter. I appreciate the quick fix. |
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I pulled v. 2.0.4's Docker image and I still get an error and termination of the segmentation when the volume is <= 0.75. |
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It's here: FastSurfer/FastSurferCNN/run_prediction.py Lines 413 to 416 in 54247b8 |
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Thanks for testing. I had fixed quick_qc to print a warning and not exit with error, but it turns out quick_qc is not actually called. Only a function from that file is called and here it is still taken as an error. This means we need to do another hot fix. Sorry for that. |
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By the way, you might be able to workaround it this time by doing the --surf_only , as that should bypass the first check. Another question: the smallest ratio you had is .72 ? |
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It's a patient population with Alzheimer's. All aged late 70s to late 90s. |
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Also, in the short term, locally I simply changed that |
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@araikes It makes sense this would work for you. One question, when you reran the subject with |
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should be solved as we now only generate warnings and reduced the threshold further. |
Question/Support Request
I have a number of individuals for whom I received the error message in the subject line. I'm trying to debug what went awry. When I overlay aseg.auto_noCCseg on orig.mgz there doesn't appear to be any obvious mis-segmentation (see example below). Is there a concise way for me to debug where these errors are coming from?
Noteworthy (maybe): I am running this on individuals with Alzheimer's. I wouldn't think this would affect the total segmentation, but perhaps.
Screenshots
Environment
Execution
singularity pull docker://deepmi/fastsurfer:2.0.1singularity exec --nv --cleanenv -B /xdisk/adamraikes/xxx/nifti:/input -B /xdisk/adamraikes/xxx/derivatives/fastsurfer-2.0.1:/output -B /groups/adamraikes/license.txt:/license.txt /groups/adamraikes/singularity_images/fastsurfer-2.0.1.sif /fastsurfer/run_fastsurfer.sh --fs_license /license.txt --t1 /input/sub-13452019/ses-10/anat/sub-13452019_ses-10_T1w.nii.gz --sid 13452019_ses-10 --sd /output --parallelThe text was updated successfully, but these errors were encountered: