kitchell / app-3dfreesurfs Goto Github PK
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License: MIT License
This application will create a 3D surface for 87 freesurfer labels from the aparc+aseg.mgz file.
License: MIT License
I just noticed that this App started producing surfaces.json containing "filename" which should be "path" according to how ui-3dsurfaces App is designed. I think it's using "path" because it could be URL.
Also, based on the updates we made to ui-3dsurfaces, the the rotation adjustment needs to happen on this App. Right now the surfaces are loaded up-side-down and off origin. I think you found a way to fix this for all freesurfer output. Can you apply the fix on this App?
Here is what it looks like now (after adjusting the filename v.s. path).
This App is currently failing with the following error message.
(on IU carbonate)
File "/N/dc2/scratch/brlife/carbonate-workflows/5dd6de8de801c93ab67d2773/5dd736a2e801c9634d7d2a0b/main.py", line 52, in <module>
niftiMask2Surface(e, aparcaseg, filename, 10, filetype)
File "/N/dc2/scratch/brlife/carbonate-workflows/5dd6de8de801c93ab67d2773/5dd736a2e801c9634d7d2a0b/niftiMask2Surface.py", line 23, in niftiMask2Surface
reader = vtk.vtkNIFTIImageReader()
AttributeError: 'module' object has no attribute 'vtkNIFTIImageReader'
ls: cannot access surfaces/*: No such file or directory
I think it's just using an old (wrong) container to run it.. Please try updating main to
export SINGULARITYENV_PYTHONNOUSERSITE=true
time singularity exec -e docker://brainlife/pythonvtk:1.1 ./main.py
(I haven't tried / tested it yet.. sorry!)
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