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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.
Luke Bloy
@bloyl
Thanks. My error actually ended up being unrelated.
Elham Khosravi
@elhamkhosravi_gitlab
Hi there, I am using ConvertScalarImageToRGB and want to use a custom_color_map_file. I have defined an array for my colormap, but couldn't make it work. Do you have an example that shows how custom_color_map_file should be defined? Thanks!
andrewcyung
@andrewcyung
Hello everybody, is it possible for me to delete just the output data in a node's directory, but configure nipype in such a way that the node will not try to run again to generate new data, nor trigger the execution of downstream nodes in the same workflow? Use case: I am running out of hard drive space, and want to clear away some intermediate data that I know I won't need anymore. However, I want to prevent reprocessing of downstream data which uses a lot of compute power. Any ideas?
Divyaashwin
@Divyaashwin

def getthreshop(thresh):
return '-thr %.10f -Tmin -bin' % (0.1 * thresh[0][1])

preproc.connect(getthresh, ('out_stat', getthreshop), threshold, 'op_string')

error: ----> preproc.connect(getthresh, ('out_stat', getthreshop), threshold, 'op_string')

NameError: name 'threshold' is not defined

matrixbot
@matrixbot
Chris Markiewicz You need to create a node named threshold to connect. Or pass the name of another node.
Divyaashwin
@Divyaashwin

Dear all,
could you please help me out to fix the issue.
I'm working on skull stripping of brain MRI dicom images.
The following program :

################PROGRAM BEGINS

from nipype.interfaces import fsl
from nilearn.plotting import plot_anat
import numpy as np
import os
import matplotlib.pyplot as plt
def bet(in_file, frac = 0.40, robust = True):
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
skullstrip = fsl.BET()
in_file = in_file
skullstrip.inputs.in_file = os.path.abspath(in_file)
skullstrip.inputs.out_file = os.path.abspath(
infile.replace('.nii.gz',
f'
{frac}_brain.nii.gz')
)
skullstrip.inputs.frac = frac
skullstrip.inputs.robust = robust
return skullstrip
anat_head = 'flair.nii.gz'
fracs = np.arange(0.3,0.75,0.05)
for frac in fracs:
skullstrip = bet(anat_head,frac = round(frac,2),)
skullstrip.run()
print(skullstrip.cmdline)

########################PROGRAM ENDS

getting following error :
Traceback (most recent call last):
File "fsl_bet.py", line 61, in <module>
skullstrip.run()
File "/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/anaconda3/lib/python3.7/site-packages/nipype/interfaces/fsl/preprocess.py", line 162, in _run_interface
runtime = super(BET, self)._run_interface(runtime)
File "/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 781, in _run_interface
% (executable_name, runtime.hostname)
OSError: No command "bet" found on host divya-HP-ProBook-440-G3. Please check that the corresponding package is installed.

matrixbot
@matrixbot
Chris Markiewicz Is FSL installed?
Divyaashwin
@Divyaashwin
yeah sir.
Peer Herholz
@PeerHerholz
are the respective environment variables set in your bashrc/bashprofile (e.g. if you type and run “fsl” within your terminal, does it work)? do you have multiple python environments?
Divyaashwin
@Divyaashwin
yeah sir. If i type fsl within the terminal(BET )works.
Divyaashwin
@Divyaashwin
I have only python3.7.6
Satrajit Ghosh
@satra
does bet work in the terminal (bet flair.nii.gz test) and are you running the python code in the same terminal (or separately through an ide)
Divyaashwin
@Divyaashwin
yeah i checked it worked
Satrajit Ghosh
@satra
are you running the code you posted in the same terminal?
can you do which bet in the terminal that you are running the code in.
Divyaashwin
@Divyaashwin
it echos "/usr/share/fsl/5.0/bin/bet"
Divyaashwin
@Divyaashwin
Dear all!!!!!!!!!!
Thank you so much . Able to fix the issue
Peer Herholz
@PeerHerholz
could you maybe post the solution (for the sake of completness)? on a related note: such question are great for https://neurostars.org/ as more folks will see your post, might be able to help and furthermore other folks with similar problems are able to find your post and thus the potential solution.
Divyaashwin
@Divyaashwin
yeah !!!!!!!!! sure
@Divyaashwin :
Divyaashwin
@Divyaashwin

@Divyaashwin ,
Step 1.

A) FSL installation is must even if we use nipype.interface for brain extration. FSL Installation link -> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation.
B) Add the following to ~/.bashrc file
. /etc/fsl/5.0/fsh.sh
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

C) After complete installation restart the system.

Step 2: Check the installation :

A) Type FSL and press enter (BET tool (GUI)pops out).
B) In command prompt , type bet inputfilename.nii.gz outfilename

If it work well, then we can use nipype.interface program for multiple slice brain extraction .

susamerz
@susamerz
Hi, I'm really new to nipype, so excuse me if I'm asking stupid questions: Is it possible to iteratively create a fslmath op string during workflow execution. I'm doing MRI analysis and my aim is to create a mask of all voxels with signal in each of a bunch of functional images from different subjects. However I don't want to hardcode how many images there are.
hardcoded I would do something like fslmath img1 -mas img2 -mas img -mas img4 outimg for four input images, where img1 has been binarized before this
christianbos1
@christianbos1
Hello, I'm also new to nipype. What packages do I need to import in order to use DualRegression()?
AishvaryaShri
@AishvaryaShri
@orduek Thank you! :)
Ari Kahn
@ariekahn
Hey, wanted to submit a quick documentation patch, but I'm seeing a number of docstring formats being used (mostly rest and numpy). What's preferred?
Ari Kahn
@ariekahn
for what it's worth, this is for a utility function, not an interface
Zvi Baratz
@ZviBaratz
Hi all! I am mentoring 2-3 students in a python course's final project / hackathon. My lab occasionally uses fsl_anat, which I couldn't find a nipype interface for. I proposed to create such an interface as a project and it was accepted, so I was wondering whether there's interest in trying to make a PR out of it.
As far as I understand there are two logical ways to create such an interface, either by subclassing FSLCommand and making the required modifications, or by checking out the source code and generating a Workflow that imitates it. Personally I think the second option is much more robust, but of course if there is interest in the PR and a strong preference for the FSLCommand method, we will gladly oblige.
Oscar Esteban
@oesteban
If you take the workflow route (which also makes more sense to me), please consider building it as a niflow (https://github.com/niflows)
niflows will basically give you a workflow manager so it can be installed as an individual application
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)?