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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!
Sin Kim
@AKSoo
is buildtemplateparallel interface in ants.legacy because nipype.workflows.smri.ants.antsRegistrationBuildTemplate replaces it?
Sin Kim
@AKSoo
nvm, got my answer. buildtemplateparallel.sh is in https://github.com/ANTsX/ANTs/wiki/Deprecated-ANTs-programs
I am still curious how closely antsRegistrationBuildTemplate follows buildtemplateparallel.sh
Sam Berry
@Sam_CBerry_twitter
Hello
I want to compute the Dice similarity between two images, I have been to this page : https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.metrics.html
but when I click on the 'link to code' it seems like it is importing libraries from a local directory (from .. import). Is this the case? How could I get this to work on my own computer? Apologies if I am missing something obvious :)
matrixbot
@matrixbot
Chris Markiewicz pip install nipype, and then, from nipype.algorithms.metrics import <interface>
Sam Berry
@Sam_CBerry_twitter
Ah I see, that worked thank you very much
leonardo-oz
@leonardo-oz
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.
nstepanovs412
@nstepanovs412
emiel8
@emiel8
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
matrixbot
@matrixbot

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 in_file, mask=True would provide -m, and 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.

Peer Herholz
@PeerHerholz
@emiel8, regarding installing nipype and the software it provides interfaces to, you can also have a look here . Installation instructions are for Ubuntu, but work well with Mac OS as well (just change the corresponding installation files). Re ANTs: I usually just download the latest release and add the paths to the .bashrc/.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 .bash thingies might be hurdle given the most likely centralized IT. based on that docker/singularity might also be out as options. let me/us know how things proceed.
emiel8
@emiel8
@PeerHerholz thank you a lot, I am going to try it ASAP this coming week and will let you know!
Grace Shearrer
@grace-shearrer
Yo! Does anyone have experience wrapping a MATLAB script in nipype? I am trying to wrap an old FSLNETS script
Tashrif Billah
@tashrifbillah
Hi, is there a documentation that explains the content of each output file from a nipype workflow?
Please see nipy/nipype#3091 for details.
Peer Herholz
@PeerHerholz
@grace-shearrer, I assume you already had a look at the examples in the nipype docs?
Tashrif Billah
@tashrifbillah
Is there a TUTORIAL showing use of DataSinkto store results in subfolders named after subject_id? This gives some hint, but no example.
Tashrif Billah
@tashrifbillah
I figured a way out from here. I am good now, thanks.
Thom Shaw
@thomshaw92
Hi experts,
I was wondering if someone could please take a look at my question over at https://neurostars.org/t/multiple-inputs-to-c3d-from-seperate-nodes/5135
Thanks so much for your help!
Sin Kim
@AKSoo
Has anyone here worked with DataSink and AWS S3 recently? I am testing the connection with a simple test file, and the file never shows up in the S3 bucket. Oddly, the workflow reports no errors. The local copy works fine too.
If one of the main developers reads this, would appreciate if he/she do a quick test on DataSink with S3 base_directory.
Sin Kim
@AKSoo
oh wow this is kind of funny
the DataSink is actually making an output directory named s3:
and putting things there
still would appreciate if someone else tests to make sure it's not a problem with my set-up
alegiac95
@alegiac95
Hello everyone, I'm having some troubles using the 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_fields input) 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!
Peer Herholz
@PeerHerholz
@alegiac95 could you provide a little more information on your pipelines, maybe including a code snippet? ants.WarpImageMultiTransform()has two mandatory inputs: input_image and 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.
alegiac95
@alegiac95
@PeerHerholz sorry i typed the wrong input name. The input is transformation_series and 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_series input (an affine and a warp) but when I provide a list as input the workflow won't run because of the error mentioned earlier
Peer Herholz
@PeerHerholz
did you check the .rst file of the corresponding node and .cmdline regarding if all other inputs are set as they should?
alegiac95
@alegiac95
@PeerHerholz I resolved it using a Merge node. Thank you for your quick support and help
Peer Herholz
@PeerHerholz
@alegiac95 glad to hear that. So it was a pipeline-input-output problem?
alegiac95
@alegiac95
@PeerHerholz yes, it was just an input-ouput problem.
EndritPJ
@EndritPJ

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!

alegiac95
@alegiac95
clear
AishvaryaShri
@AishvaryaShri
can functional connectivity be calculated in rsfMRI using nipype
Hailey Trier
@trier1_gitlab
Hi, possibly silly question here - nipype can't find the executable file 'feat_model' from fsl, even though it's definitely in my fsl file - any suggestions? i must be missing a simple command
matrixbot
@matrixbot
Chris Markiewicz Not sure what you mean by "in your FSL file"... Is feat_model runnable from the same shell you're running nipype from?
Sudhakar Tummala
@Tummala1985_twitter
Hello, How to convert zipped dicom folder to Nifti in Nipype?
matrixbot
@matrixbot
Chris Markiewicz There's a dcm2niix interface in Nipype.
Or Duek
@orduek
@AishvaryaShri Nilearn might be you best bet for those ones
Luke Bloy
@bloyl
Not sure if here or neurostars or github is the best to ask questions but I’ll start here :)
Can I use a joinNode to merge the outputs of a mapNode? I feel like I should but haven’t seen it in any of the docs?
matrixbot
@matrixbot
Chris Markiewicz Nope. JoinNode's collapse workflows split by an iterable. You can think of a MapNode as a single-node split and join. The outputs are always promoted to lists.