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nipy / nipype

Workflows and interfaces for neuroimaging packages
https://nipype.readthedocs.org/en/latest/
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nipype issues with calling dcm2nii #3302

Open Gresliebear opened 3 years ago

Gresliebear commented 3 years ago

nipype noob here thank you for developing this software packages its very help but I am running to into simply problem by reading in a source_dir PAT001 containing 201 dcm files convert into nii file for developing pipeline for a deeplearning model

OSError: [WinError 10038] An operation was attempted on something that is not a socket

Summary

# change these for your system
dcm_folder = 'D:\L_pipe\DataScienceDeck\DataScienceDeck\Data\Data_input\PAT001' ## our input is the number 201 dcm files 
output_folder = 'D:\L_pipe\DataScienceDeck\DataScienceDeck\Data\Data_output\output_nifti'

def convert_dcm_2_nii_x(dcm_folder, output_folder):
    converter = Dcm2niix()

    print(len(dcm_folder))

    converter.inputs.source_dir = dcm_folder
    converter.inputs.output_dir = output_folder
    converter.inputs.compress = 'i'
    converter.run()
    return print("done")

from nipype.interfaces.dcm2nii import Dcm2nii

Actual behavior

210216-11:28:56,30 nipype.interface INFO:
         [WinError 10038] An operation was attempted on something that is not a socket
Traceback (most recent call last):
  File ".\dcm2nifti.py", line 50, in <module>
    convert_dcm_2_nii_x(dcm_folder, output_folder)
  File ".\dcm2nifti.py", line 26, in convert_dcm_2_nii_x
    converter.run()
  File "D:\L_pipe\pipeline_env\lib\site-packages\nipype\interfaces\base\core.py", line 434, in run
    runtime = self._run_interface(runtime)
  File "D:\L_pipe\pipeline_env\lib\site-packages\nipype\interfaces\dcm2nii.py", line 445, in _run_interface
    runtime, correct_return_codes=(0, 1,)
  File "D:\L_pipe\pipeline_env\lib\site-packages\nipype\interfaces\base\core.py", line 827, in _run_interface
    runtime = run_command(runtime, output=self.terminal_output)
  File "D:\L_pipe\pipeline_env\lib\site-packages\nipype\utils\subprocess.py", line 137, in run_command
    _process()
  File "D:\L_pipe\pipeline_env\lib\site-packages\nipype\utils\subprocess.py", line 124, in _process
    res = select.select(streams, [], [], timeout)
OSError: [WinError 10038] An operation was attempted on something that is not a socket

I am pretty sure dcm2nii code is running because it generates a bunch of .nii files image

Expected behavior

image

Script/Workflow details

taking 200 DICOM files into a single nii file

Platform details:

Windows 10 VScode python 3.7

Execution environment

Choose one

athertya commented 3 years ago

I have the same issue and error,windows socket error. How to solve ?

effigies commented 3 years ago

Hi, the problem is that we don't support Windows (this is issue #3277). We'd be happy to accept a patch from someone with a Windows machine. You can also try using the Windows Subsystem for Linux (WSL), but I don't have any experience there.

Gresliebear commented 3 years ago

it will be a weekend project for me when I get around to it after work.

athertya commented 3 years ago

Thank you for getting back on this issue. @Gresliebear That would be great. Please do keep me posted.

TamerGezici commented 2 years ago

Hi. Is there any news on the compatibility of dcm2niix for windows? The socket error still persists for me. As I mentioned in this issue: https://github.com/rordenlab/dcm2niix/issues/609

effigies commented 2 years ago

I have recently come into possession of a Windows machine, so when I have the opportunity, I can try to debug this. Making nipype Windows compatible will be a major effort, though. Have you looked into Pydra? Or using the WSL?

yarikoptic commented 1 year ago

any luck ? it seems there are more users hitting this: https://neurostars.org/t/dcm2niix-error-using-heudiconv/26759