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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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Oscar Esteban
@oesteban
ping @effigies for further information
Yasmin Aljedawi
@jasminej90
Hello, I am new to nipype. Can I use it with anaconda 3.7? Or is it strict to 2.7 (since FSL is compatible with python 2.7 only but not 3.X)?
Peer Herholz
@PeerHerholz
@jasminej90 yeah, nipype is a workflow enginge and “only” wraps FSL (and many other) functions. As long as your FSL installation can be sourced respectively, you should be good to go. Also, for such questions we recommend to use neurostars.org wrt archiving and findability.
Sudhakar Tummala
@tummala_gitlab
Hello all, is it possible to use T2 or FLAIR images along with T1 for SPM segment? I could not see an option at the moment in Nipype, if anybody has used it, please let me know.
Sudhakar Tummala
@tummala_gitlab
which version of Nipype has got MultiChannelNewSegment?
Ben Velie
@veliebm
hi guys! i'm struggling to transfer my pi's lab to nipype. he said nipype can automatically determine the best interface for any preprocessing step. for example, if afni has the best blurring step, then nipype should automatically use afni's interface to blur our images. but i've been fiddling with the software for a week now and i haven't figured out how to get it to do that. can nipype actually choose the best interfaces on its own?
appreciate your time 🙂
matrixbot
@matrixbot
Chris Markiewicz Nipype gives you the ability to easily switch from one tool to the other, if you decide one is better, but nipype has no way to determine "best" or automatically switch. You could create a workflow that performs several steps, and then selects one result using some objective function...
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