Issues with createSurface.py #6
Comments
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Hello, thanks for your message. I speculate that the issue may be due to using the |
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Thank you! That got me a bit further but now I have a new error - do you know what this might be now? Computing cube parametrization --> VTK format ... --> VTK format ... TriaMesh with anisotropic Laplace-Beltrami |
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Hm, this may be a bit more tricky. Could you maybe post the command that you used for running the software? |
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Thank you! This is the command that I gave:
And this was the entire output `----------------------------------------
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Thank you very much. I have to admit that I am a bit at a loss at the moment, and see no obvious reason for the processing failure. If you can share the particular segmentation file that produces the error I am happy to take a closer look while trying to replicate the issue. |
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Thank you so much! Could I get your email to share it with you please?
…On Thu, Jun 6, 2024 at 9:55 AM Kersten Diers ***@***.***> wrote:
Thank you very much. I have to admit that I am a bit at a loss at the
moment, and see no obvious reason for the processing failure. If you can
share the particular segmentation file that produces the error I am happy
to take a closer look while trying to replicate the issue.
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Please find my email on our lab's webpage (trying to post it not on too many different places). |
The freesurfer files that I'm trying to run Hipsta on are from Freesurfer7.2 labeled: rh.hippoAmygLabels-T1.v21.CA.mgz, lh.hippoAmygLabels-T1.v21.CA.mgz
When looking at results through freeview these files are either unable to open or blank:
but lh.image.mgz seems to be fine
This is the error I'm getting:
`Smooth surface
--> VTK format ...
[file not found or not readable]
[ERROR: hipsta.py] Error Information:
[ERROR: hipsta.py] Type: <class 'AttributeError'>
[ERROR: hipsta.py] Value: ("'NoneType' object has no attribute 'rm_free_vertices_'",)
Traceback (most recent call last):
File "/Users/joshuanguyen/.pyenv/versions/3.10.11/envs/myenv/bin/run_hipsta", line 8, in
sys.exit(main())
File "/Users/joshuanguyen/.pyenv/versions/3.10.11/envs/myenv/lib/python3.10/site-packages/hipsta/cli/init.py", line 26, in main
_run_hipsta(args)
File "/Users/joshuanguyen/.pyenv/versions/3.10.11/envs/myenv/lib/python3.10/site-packages/hipsta/hipsta.py", line 840, in _run_hipsta
run_analysis(params)
File "/Users/joshuanguyen/.pyenv/versions/3.10.11/envs/myenv/lib/python3.10/site-packages/hipsta/hipsta.py", line 743, in run_analysis
params = smoothSurface(params)
File "/Users/joshuanguyen/.pyenv/versions/3.10.11/envs/myenv/lib/python3.10/site-packages/hipsta/createSurface.py", line 272, in smoothSurface
triaMesh.rm_free_vertices()
AttributeError: 'NoneType' object has no attribute 'rm_free_vertices'`
Please advise
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