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BioMedIA / dhcp-structural-pipeline

structural analysis of neonatal brain MRI scans
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Segmentation error #2

Open ajdneuro12 opened 5 years ago

ajdneuro12 commented 5 years ago

Hi all,

Thank you for sharing this pipeline. I am trying to run it on my neonate data (infants scanned within 3 months of birth). I formatted my data to match the suggested command to run it in docker. I am running it on Windows 10 but I also got the same error on my mac (Sierra). I have attached the log. Thank you for your help! Best, Alex subject1-session1.segmentation.log

whinds commented 5 years ago

Hello,

Thank you for creating this pipeline. After successful segmentation, when it begins the surface reconstruction part I have the following error:

pipeline/build/MIRTK/build/lib/python/mirtk/deformable/neonatal_cortex.py", line 213, in output else: path = name_or_func() TypeError: 'unicode' object is not callable Error: recon-neonatal-cortex command returned non-zero exit status 1

I deleted the parenthesis so the line 213 now reads else: path = name_or_func

This fix allows the surface pipeline to run now, but I want to double check with you the developers. Additional info, I am running this code on Ubuntu 18.1 from a virtual machine.

ajdneuro commented 5 years ago

Hi all,

It seems it is getting to the tissue priors step and failing: /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/scripts/tissue-priors.sh subject1-session1 44 non-rigid-v2 8 : failed /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/pipelines/neonatal-pipeline.sh /data/workdir/subject1-session1/T2/subject1-session1.nii.gz 44 -t 8 -c 1 -p 1 -v 1 -atlas non-rigid-v2 : failed

Any ideas? I made sure I pulled the most recent docker image. Thanks!

Best, Alex