Errors at end of fmriprep pipeline in flywheel

Hi,

I am trying to use the fmriprep pipeline for my fmri study. The scanning centre provides this as a service in their flywheel.io platform, but it seems i run into some errors right at the end of my preprocessing pipeline. I am posting this in the hope somebody else knows how to solve this problem. If not, thanks for reading anyway!

After a few hours of processing the run-log gives this as ‘errors’ in red. I am using the fmriprep version v5.7.1_1.2.6-1. Does anybody know what the problem can be and if i can solve this? Thanks! If anybody needs some additional information, please let me know.

Kind regards,

‘error’=

/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from ‘collections’ instead of from ‘collections.abc’ is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nitime/utils.py:980: FutureWarning: Conversion of the second argument of issubdtype from complex to np.complexfloating is deprecated. In future, it will be treated as np.complex128 == np.dtype(complex).type.
complex_result = (np.issubdtype(in1.dtype, np.complex) or
/usr/local/miniconda/lib/python3.7/site-packages/scipy/fftpack/basic.py:160: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
z[index] = x
/usr/local/miniconda/lib/python3.7/site-packages/skimage/init.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/usr/local/miniconda/lib/python3.7/site-packages/pytest.py’ mode=‘r’ encoding=‘utf-8’>
imp.find_module(‘pytest’)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from ‘collections’ instead of from ‘collections.abc’ is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/init.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/usr/local/miniconda/lib/python3.7/site-packages/pytest.py’ mode=‘r’ encoding=‘utf-8’>
imp.find_module(‘pytest’)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nitime/utils.py:980: FutureWarning: Conversion of the second argument of issubdtype from complex to np.complexfloating is deprecated. In future, it will be treated as np.complex128 == np.dtype(complex).type.
complex_result = (np.issubdtype(in1.dtype, np.complex) or
/usr/local/miniconda/lib/python3.7/site-packages/scipy/fftpack/basic.py:160: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
z[index] = x
/usr/local/miniconda/lib/python3.7/site-packages/nitime/utils.py:980: FutureWarning: Conversion of the second argument of issubdtype from complex to np.complexfloating is deprecated. In future, it will be treated as np.complex128 == np.dtype(complex).type.
complex_result = (np.issubdtype(in1.dtype, np.complex) or
/usr/local/miniconda/lib/python3.7/site-packages/scipy/fftpack/basic.py:160: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
z[index] = x
/usr/local/miniconda/lib/python3.7/site-packages/nitime/utils.py:980: FutureWarning: Conversion of the second argument of issubdtype from complex to np.complexfloating is deprecated. In future, it will be treated as np.complex128 == np.dtype(complex).type.
complex_result = (np.issubdtype(in1.dtype, np.complex) or
/usr/local/miniconda/lib/python3.7/site-packages/scipy/fftpack/basic.py:160: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
z[index] = x
Preprocessing did not finish successfully. Errors occurred while processing data from participants: PIN143 (1). Check the HTML reports for details.
Sentry is attempting to send 2 pending error messages
Waiting up to 2.0 seconds
Press Ctrl-C to quit
Captured warning (<class ‘ResourceWarning’>): unclosed <socket.socket fd=7, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6, laddr=(‘10.164.0.44’, 45404), raddr=(‘35.188.42.15’, 443)>

real 245m38.765s
user 13m50.932s
sys 0m3.114s

Hi @Zyveon. I would probably try talking to your sysadmins. By the version string, it looks like they’re building a custom version of fMRIPrep. The errors you show list a number of warnings but no errors. They may be better situated to help you.

Hi @effigies, thanks for getting back to me!

Would you think it is at all possible to use the setting save_outputs and use that for my analysis? (since there were no real errors?) Ill also talk to my admin, but not sure if he knows much about this :slight_smile:

Thanks anyway,

Kind regards

Hi @Zyveon, it’s difficult to give advice about Flywheel, which is not a system I’m familiar with. If it has a save_outputs option, that seems like a good idea.

Hi @Zyveon , I think you are using Penn flywheel. It is important to check if the particular subject passed bids validation, and the fmriprep has been updated to 1.5.2 on flywheel. @mattcieslak

@a3sha2 it looks like this is the flywheel-maintained version of fmriprep, not ours. @Zyveon you should file a bug report with support@flywheel.io if no outputs are being produced. BIDS validation is a good first check and to echo @effigies, the save_outputs option is very helpful in situations like this. It also looks like there weren’t any actual errors.

he mentioned the version v5.7.1_1.2.6-1

Hi all,

Sorry for the late response. I had a few weeks off.
I am pretty sure the files passed BIDS validation, but i cannot update my flywheel. This is something i am working on with the administrator. If this doesnt work ill just make a manual SPM12 script.

Thanks for all your help!