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Mohit Saxena
@mohitindelhi_gitlab
Can someone tell how to get FSLeyes working?
matrixbot
@matrixbot
Chris Markiewicz I think neurostars.org (or the FSL mailing list) will be a better forum for this question. FSLeyes is an FSL project, not a part of nipype.
Mohit Saxena
@mohitindelhi_gitlab
how to view these images then
One more question? Can anyone tell how to use the argument flags for example in Brain extraction (BET) the flags -R for robust. I twould be great if you could send an example of using flags..
Elizabeth DuPre
@emdupre
but BET is also from FSL, so their mailing list should be a good place for that question as well !
Or at least the BET docs :) https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide Hope that helps !!
Mohit Saxena
@mohitindelhi_gitlab
I have seen this. I have been using bash scripts previously using FSl command line. But nipype seems to be a lot more different when it comes to using flags. if anyone has used the flags somewhere in there script i would appreciate if they could share the usage of the flags. The BET example however talks about he flags but the usage is restricted to the Fractional intesity threshold. I need an example how to use -R (as in bash)
Elizabeth DuPre
@emdupre
you would use it in exactly the same way. See the interface specification -- it's "robust"
so in the interface example it would be btr.inputs.robust = True
Mohit Saxena
@mohitindelhi_gitlab
nut Frac has a numerical value
Elizabeth DuPre
@emdupre
yes, it's a boolean, as described in the docs :)
Mohit Saxena
@mohitindelhi_gitlab
ohh thanks a lot
Elizabeth DuPre
@emdupre
it being "robust"
glad that helped :+1:
Mohit Saxena
@mohitindelhi_gitlab
Thanks!!
Thatworked
Elizabeth DuPre
@emdupre
:tada:
sneha-dg
@sneha-dg
Hi, How do you write the following command line code in nipype? %%bash
fslnvols /data/sub-01/func/sub-01_task-obj_bold.nii.gz
Abel González
@abelalez
@sneha-dg I'm not sure if there is a Nipype function of fslnvols. But, you can use the package NiBabel to know the dimensions of your image.
import nibabel
img = nibabel.load("your_image.nii")
img.shape
Mohit Saxena
@mohitindelhi_gitlab
HI how does one use fsleyes through nipype? Is there any other interface to view th eouputs of?
sneha-dg
@sneha-dg
@abelalez this worked! Thanks a lot
Peer Herholz
@PeerHerholz
@mohitindelhi_gitlab, as already pointed out by @effigies such questions are great for neurostars.org (as more people will be able to help and benefit from it) and FSLeyes is not part of nipype. I would suggest you look into nibabel and nilearn. Especially the latter provides an amazing and divers functionality to plot all sorts of brain imaging data
matrixbot
@matrixbot
Chris Gorgolewski This looks like an interesting model for nipype: https://nf-co.re/ Satrajit Ghosh (Gitter)
fabioboh
@fabioboh
dear all,
I would like to use the spm.FieldMap interface in nipype to correct some fMRI epi images for inhomogeneities in the magnetic field
I guess I can run FieldMap, first setting jobtype calculatevdm
then applyvdm
however from the documentation it is not so clear to me this would work as as output only a vdm file is given
fabioboh
@fabioboh
should not tthere be also an unwarped epi image?
Horea Christian
@TheChymera
hi guys, how can I signal that an attribute of an inputspec will require another one to be present?
matrixbot
@matrixbot
Chris Markiewicz Requires
Kuang-Han Huang
@kuanghan
Hi everyone, thanks a lot for the hard work! One question about the SPM interface's slice timing parameter (nipype.interfaces.spm.SliceTiming): documentation says the parameter for the reference slice ref_slice needs to be of type int, but then it says it could be a 1-based index or a reference time point in msec (which would be a float). Right now, it throws an error when I try to use a time point for ref_slice, which would be a float (because I'm using TR/2). Maybe the input type for ref_slice should be changed? SPM12 takes either an integer or float, so ideally nipype should take either an integer or float as well. Thanks!!
fabioboh
@fabioboh
ok I will try to add the applyvdm functionality to the fieldmap interface
Victor Férat
@vferat
Hi everyone, I would like to wrap a python function with an input that can be Either a list or a Str, and i would like to set a default value. But when i call method.default_values, the console returns undefined
There is my code sample:
My_input = traits.Either(traits.ListStr(('a', 'b'),usedefault=True), traits.Str(), desc='''description''', mandatory=False, usedefault=True)
In tthis exemple, i would like to have the list ("a","b) as default value
Thanks for you help and for all the work you are doing on nipype !
Victor Férat
@vferat
Found the soluton, I can set-up the default avalue using "default="
Seems pretty obvious..
andrewcyung
@andrewcyung
Hi there, forgive me if this is the wrong place to ask this - I am having trouble using a Slicer interface (from nipype.interfaces.slicer.registration.brainsresample.BRAINSResample) because the workflow is not detecting the command. I do realize that BRAINSResample is a Slicer module, and can call it on the command line by going to the Slicer install directory and typing "./Slicer --launch BRAINSResample". I suspect that there is a problem with the visibility of the BRAINSresample module. Is it fair to say that if I can type "BRAINSResample" in a terminal window in any directory, then nipype should be able to call it? Note that I do have the Slicer path defined in the PATH environment variable in my ~.bashrc file - but I'm not sure if my python installation sees this environment variable?
Casa Mofoekeng 'Moso
@CasaMofoekengMo_twitter
@CasaMofoekengMo_twitter
Hello, I am trying to implement Python code when given the names and GPS positions of 750 people (latitude, longitude, and elevation) to find the names of the 10 closest neighbors of a randomly selected individual.
please help.
kenneth dombrowski
@kennethd
hello, i have a project which depends on numpy<=1.14.3, as well as fitz, which depends on nipype, pip attempts to install nipype 1.2.1, which then errors out with error: numpy 1.14.3 is installed but numpy>=1.15.3 is required by {'nipype'} which is strange because i see in the nipype requirements.txt depends on numpy>=1.9.0, so i wonder if it is something about your travis environment causing the egg to require a later version? if i examine the EGG_INFO in my site-packages, it does indeed depend on 1.15.3:
/opt/docker/ocrolus-core # grep numpy /usr/lib/python3.7/site-packages/nipype-1.2.1-py3.7.egg/EGG-INFO/requires.txt
numpy>=1.15.3
Chris Markiewicz
@effigies
Numpy had an issue that only exhibited in Python 3.7, which was fixed in 1.15.3: https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
If you need an earlier numpy, you should probably revert to Python 3.6.
kenneth dombrowski
@kennethd
@effigies thanks, it built with nipype<=1.2.0, i will check out the link though
kenneth dombrowski
@kennethd
@effigies the 3.7 on our alpine images don't display any of those errors, btw
Chris Markiewicz
@effigies
It looks like that constraint has been in place since 1.1.8 (nipy/nipype@2bd4fc2), so I don't know what would be new.
Julio Cesar de Azeredo
@jcazeredo

Is it good to use Nipype for non-neuroimaging applications? I think Nipype amazing and so simple for creating pipelines and workflows, is there a similar library for this that is for general use and provide functionalities like creating workflows and nodes? Or can I use Nipype to create workflows with my own Python's functions?

Thank you

Chris Markiewicz
@effigies
Yup, the core of nipype isn't really neuroimaging specific. Most of nipype.algorithms and nipype.interfaces will be neuroimaging-related, but even there you have things like nipype.interfaces.base, nipype.interfaces.io, and nipype.interfaces.utility that are pretty generic.
Julio Cesar de Azeredo
@jcazeredo
@effigies Even using my own functions as nodes, can Nipype parallelize my workflow (if nodes are not dependent)?
Chris Markiewicz
@effigies
Yes. To be clear, you'll want to use the Function interface to wrap your functions (or check out the SimpleInterface interface to make a fully-fledged interface that is pretty low-boilerplate), but yes, most Python functions can be sensibly turned into Nipype interfaces.
Julio Cesar de Azeredo
@jcazeredo
@effigies That's nice, thank you!