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  • Nov 23 16:43
    codecov[bot] commented #3267
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    codecov[bot] commented #3267
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    FIX: Purge BaseException.message FIX: Get OSError.errno by name,… Merge pull request #3272 from e… (compare)

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    codecov[bot] commented #3273
Ben Velie
@veliebm
rats! oh well. thanks for answering me!
Abdul Sayyed
@AbdulSayyed
Hi, I am new to nipype and trying to follow a given example but when I read a file using BET interfaces I constantly get a trait error.
TraitError: The 'in_file' trait of a BETInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz' was specified.
Any help !
from nipype.interfaces.fsl import BET
skullstrip = BET(in_file=fileInput)
res = skullstrip.run()
print(res.outputs.out_file)
matrixbot
@matrixbot
Chris Markiewicz If that's a datalad dataset, it's possible that the data is not fetched. Can you open that file with any other tool?
Abdul Sayyed
@AbdulSayyed
Yes I can open it if I move the file to my current directory
matrixbot
@matrixbot
Chris Markiewicz I'm not sure I understand. Does something prevent you from opening in its initial location?
Abdul Sayyed
@AbdulSayyed
on line 2 above skullstrip = BET(in_file = fileInput) it throws the above error
matrixbot
@matrixbot
Chris Markiewicz Sorry, I was unclear. I meant, why do you need to move the file to your current directory to open it? What are you using to open it?
Abdul Sayyed
@AbdulSayyed
I am not moving it, I am trying to read it where it is but it does not read it from the original location, for some reason it says that a path like object is expected .. but the value of ... is specified
matrixbot
@matrixbot
Chris Markiewicz
What do you get if you run: ls -AFl /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz
Abdul Sayyed
@AbdulSayyed
The file is in the directory /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz but the function does not treat it an acceptable path.
matrixbot
@matrixbot
Chris Markiewicz Ah. What is fileInput, then? Is there a chance that you're missing an initial /?
Abdul Sayyed
@AbdulSayyed
Thanks I got the point it is link pointing to another location let me deal with it , if any problem I will come back many thanks
Rami Hamati
@ramroomh
Hi there, thanks for your time. Looking to wrap https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register. It is 1 line in bash, with the only required flag being subject ID -freesurfer does the rest. Is there any quick way to add this to a work flow without creating a whole interface?
Renata Baptista
@rpbaptista
Hello, I wondered if I could import the whole fsl_anat() with nipype, thanks!
Peer Herholz
@PeerHerholz
@ramroomh you could use the function interface for that: https://miykael.github.io/nipype_tutorial/notebooks/basic_function_interface.html
workflows that used to be available via nipype.workflows were migrated to NiFlows and their continued use is discouraged: https://nipype.readthedocs.io/en/latest/interfaces.html#workflows
Peer Herholz
@PeerHerholz
Renata Baptista
@rpbaptista
Yes I saw that I can't use directly, would you recomend a way for transfering fsl_anat to be nipype adaptable?
Peer Herholz
@PeerHerholz
AFAIK all the functions in fsl_anat are supported by/available in nipype, thus you could just "recreate" the pipeline there. However, I'm not sure if that's more feasible than using FSLCommand or the function interface. I would assume that someone also already looked at that!?
@ramroomh and @rpbaptista, it would be great if you could post nipype related questions on https://neurostars.org/ to increase FAIR-ness and reach more people
Renata Baptista
@rpbaptista
It's really not clear to me how to use interfaces for that, once is a shell script not a python package, like if its to do os..... i can do outside nipype. For the FSL COMMANDS I also don't know how to associate, there's no example on documentation..
amir
@liamirpy
hi
i cant find trans.mat
Boojum
@intein
Nipype is amazing, thank you all! I've just started using it and I like it more and more
1 reply
kevinm36
@kevinm36

Hi, I hope this is the correct place to ask simple questions.

How exactly do you handle Nodes that take in lists as inputs within a workflow? Specifically, I'm trying to append the apply_to_files property for the spm.normalization interface from the output of two different nodes.

2 replies