Comments (2)
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.
from dhcp-structural-pipeline.
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
from dhcp-structural-pipeline.
Related Issues (20)
- Surface Reconstruction FAILED, please suggest new parameter values for gaus_curvature and min_width
- Non rigid step failing HOT 2
- exporting surface files (*.dscalar.nii or *.shape.gii) to freesurfer format HOT 1
- Tissue probability maps are not correctly copied
- Error with T1w/T2w maps
- Segmentation error (with docker image) HOT 10
- Surface error under docker image
- Error with dhcp-structural-pipeline:fetal in docker
- Native install on Big Sur
- Segmentation error HOT 3
- Installation difficulties HOT 1
- Calculate curvature in the script process-surfaces-hemisphere
- Infant structural T1 data segmentation HOT 1
- mirtk padding failure for tissue labels
- setup.sh Failure HOT 1
- setup.sh failure
- code version for dHCP release 3? HOT 3
- Pipeline outputs
- docker issue apple silicon chips?
- recon-neonatal-cortex error HOT 8
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from dhcp-structural-pipeline.