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    codecov[bot] commented #3275
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  • Nov 23 13:07
    effigies commented #3272
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.
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.