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?
nipype.interfaceswill be neuroimaging-related, but even there you have things like
nipype.interfaces.utilitythat are pretty generic.
Chris Markiewicz > <@gitter_emiel8:matrix.org> Hello. I want to use the nipype.interfaces.ants for my master thesis because the ANTs toolbox has a lot of very good functions for MR brain images. However I was wondering what is necessary to be installed on the computer to use this nipype.interfaces.ants command. I looked for it myself but I am not an expert in this kind of stuff. The computers in school are on Mac OS and I need some good explanation before I am allowed to install something on them. I found this (https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS) page about compiling ANTs on Mac OS. Would this be enough to call ants functions through nipype in python ? My excuses if I don't see the obvious here, but I am not that familiar with this kind of stuff. Thanks in advance
Yes, if you have ANTs installed and can call the programs from the command line, then nipype should be able to call them as well.
Chris Markiewicz > <@gitter_leonardo-oz:matrix.org> Hello. In fsl terminal, I can run 'bet t1.nii.gz out -m -A2 t2.nii.gz' for surface creation with both T1 and T2, How could I write the similar code in nipype? Thanks.
Looks like t1.nii.gz would be the
mask=True would provide
t2_guided='t2.nii.gz' would provide
-A2 t2.nii.gz. See https://nipype.readthedocs.io/en/latest/interfaces/generated/interfaces.fsl/preprocess.html#bet.
Chris Markiewicz > <@gitter_nstepanovs412:matrix.org> http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data2.tar.gz It does not work
Could you please open an issue with where we link to that and an updated link, if you know it? If you can't find one, you can ask on the FSL mailing list where that data can now be found.
.bash_profile. So far I did not need to compile it on Mac OS. That being said: newer versions (looking at you catalina) might create problems. If you want to use computers at your school the mentioned
.bashthingies might be hurdle given the most likely centralized IT. based on that
singularitymight also be out as options. let me/us know how things proceed.
DataSinkto store results in subfolders named after
subject_id? This gives some hint, but no example.
ants.WarpImageMultiTransform()interface. The problem I'm having is that one of the input fields of this interface is supposed to be composed of multiple files (
in_fieldsinput) but as soon as I run the pipeline I get an
TypeError: unhashable type: 'list'error. How can I avoid this? Thank you so much for your help!
ants.WarpImageMultiTransform()has two mandatory inputs:
transformation_series. The first should an image (e.g., a structural or a functional) and the second a list of files representing the transformation files.
transformation_seriesand I'm using it to apply some transformations that I already have obtained from the generation of an ants template to a functional image. The problem is that to transform correctly the image I have to provide two inputs in the
transformation_seriesinput (an affine and a warp) but when I provide a list as input the workflow won't run because of the error mentioned earlier
Hello! I have a question regarding nipype - I found the c3d wrapper to be missing lots of functions such as thresholding: https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.c3.html
Is there any way I can access all c3d functions from the nipype module? If not are there any plans to add this? Thank you!