Hello,
I have been trying to run heudiconv on my dcm data. However, I keep having this problem whenever I add the dcm2niix line into my terminal. I have tried to solve this problem by working offline, making sure I do not have any other softwares running, but this error keeps occuring. If anyone knows how to resolve this problem, it would be much appreciated!
Thank you.
heudiconv --files "C:\Users\S\Desktop\TEST" -o "C:\Users\S\Desktop\bids" -s test -c dcm2niix -b -f "C:\Users\S\Desktop\TEST\myh.py" C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.9) or chardet (5.2.0)/charset_normalizer (2.0.12) doesn't match a supported version! warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported " INFO: Running heudiconv version 0.13.1 latest 0.13.1 INFO: Analyzing 4548 dicoms WARNING: Ignoring C:\Users\S\Desktop\TEST\__pycache__\myh.cpython-39.pyc since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING: Ignoring C:\Users\S\Desktop\TEST\desktop.ini since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING: Ignoring C:\Users\S\Desktop\TEST\myh.py since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' INFO: Generated sequence info for 1 studies with 17 entries total WARNING: Heuristic is missing an infotoidsmethod, assigning empty method and using provided subject id test. Providesessionandlocator` fields for best results.
INFO: Study session for StudySessionInfo(locator=None, session=None, subject=‘test’)
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {‘subject’: ‘test’, ‘outdir’: ‘C:\Users\S\Desktop\bids\’, ‘session’: None}
INFO: Processing 17 pre-sorted seqinfo entries
INFO: Doing conversion using dcm2niix
INFO: Converting C:\Users\S\Desktop\bids\sub-test/anat/sub-test_T1w (1 DICOMs) → C:\Users\S\Desktop\bids\sub-test/anat . Converter: dcm2niix . Output types: (‘nii.gz’, ‘dicom’)
230915-15:49:44,224 nipype.workflow INFO:
[Node] Setting-up “convert” in “C:\Users\S\AppData\Local\Temp\dcm2niixl6jsq2b_\convert”.
INFO: [Node] Setting-up “convert” in “C:\Users\S\AppData\Local\Temp\dcm2niixl6jsq2b_\convert”.
230915-15:49:44,271 nipype.workflow INFO:
[Node] Executing “convert” <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing “convert” <nipype.interfaces.dcm2nii.Dcm2niix>
230915-15:49:44,413 nipype.interface INFO:
[WinError 10038] An operation was attempted on something that is not a socket
INFO: [WinError 10038] An operation was attempted on something that is not a socket
230915-15:49:44,413 nipype.workflow INFO:
[Node] Finished “convert”, elapsed time 0.015621s.
INFO: [Node] Finished “convert”, elapsed time 0.015621s.
230915-15:49:44,413 nipype.workflow WARNING:
Storing result file without outputs
WARNING: Storing result file without outputs
230915-15:49:44,420 nipype.workflow WARNING:
[Node] Error on “convert” (C:\Users\S\AppData\Local\Temp\dcm2niixl6jsq2b_\convert)
WARNING: [Node] Error on “convert” (C:\Users\S\AppData\Local\Temp\dcm2niixl6jsq2b_\convert)
Traceback (most recent call last):
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\runpy.py”, line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\runpy.py”, line 87, in run_code
exec(code, run_globals)
File "C:\Users\S\AppData\Local\Programs\Python\Python39\Scripts\heudiconv.exe_main.py", line 7, in
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\cli\run.py”, line 30, in main
workflow(**kwargs)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\main.py”, line 463, in workflow
prep_conversion(
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\convert.py”, line 255, in prep_conversion
convert(
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\convert.py”, line 616, in convert
res, prov_file = nipype_convert(
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\convert.py”, line 829, in nipype_convert
eg = convertnode.run()
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\pipeline\engine\nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\pipeline\engine\nodes.py”, line 645, in _run_interface
return self._run_command(execute)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\pipeline\engine\nodes.py”, line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node convert.
Cmdline:
dcm2niix -b y -z y -x n -t n -m n -f sub-test_T1w_heudiconv391 -o C:\Users\S\Desktop\bids\sub-test\anat -s n -v n C:\Users\S\AppData\Local\Temp\dcm2niixl6jsq2b_\convert
Stdout:
Stderr:
Traceback:
Traceback (most recent call last):
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\interfaces\base\core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\interfaces\dcm2nii.py”, line 445, in _run_interface
runtime = super(Dcm2niix, self)._run_interface(
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\interfaces\base\core.py”, line 764, in _run_interface
runtime = run_command(
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\utils\subprocess.py”, line 141, in run_command
_process()
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\nipype\utils\subprocess.py”, line 128, in _process
res = select.select(streams, , , timeout)
OSError: [WinError 10038] An operation was attempted on something that is not a socket
Exception ignored in: <function TempDirs.del at 0x00000273F79B0820>
Traceback (most recent call last):
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\utils.py”, line 102, in del
self.cleanup()
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\utils.py”, line 114, in cleanup
self.rmtree(t)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\site-packages\heudiconv\utils.py”, line 119, in rmtree
shutil.rmtree(tmpdir)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\shutil.py”, line 759, in rmtree
return _rmtree_unsafe(path, onerror)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\shutil.py”, line 624, in _rmtree_unsafe
_rmtree_unsafe(fullname, onerror)
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\shutil.py”, line 633, in _rmtree_unsafe
onerror(os.rmdir, path, sys.exc_info())
File “C:\Users\S\AppData\Local\Programs\Python\Python39\lib\shutil.py”, line 631, in rmtree_unsafe
os.rmdir(path)
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\S\AppData\Local\Temp\dcm2niixl6jsq2b\convert’`
I keep finding dcm2niix temp files in my system that does not have anything in their convert folder.