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Description
Summary
Originally observed by @dnkennedy while running heudiconv on what appears to be incomplete series. then reproduced on some shorter case of 3 slices dicoms picked up from 10k of them (can't share, didn't find any public ones).
Actual behavior
The point is that if we have
❯ cd /tmp/ttt
MR.1.3.12.2.1107.5.2.43.167017.2020012914293355999131660 MR.1.3.12.2.1107.5.2.43.167017.2020012914301930881739443 MR.1.3.12.2.1107.5.2.43.167017.2020012914320550634554326
❯ dcm2niix -z y .
Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC12.1.0 x86-64 (64-bit Linux)
Found 3 DICOM file(s)
Slices stacked despite coil variation 'H1' vs 'H7' (use '-m o' to turn off merging)
Warning: Interslice distance varies in this volume (incompatible with NIfTI format).
Warning: Missing images? Expected 3 images, but instance number (0020,0013) ranges from 23 to 136
Convert 3 DICOM as ./_swi_acq-QSMX3echos_20200129132019_26_cH11_ph (264x288x3x1)
Warning: Unable to rotate 3D volume: slices not equidistant: 40 != 73
Compress: "/usr/bin/pigz" -n -f -6 "./_swi_acq-QSMX3echos_20200129132019_26_cH11_ph.nii"
❯ echo $?
1reproducing execution with nipype:
import random
from nipype import Node
from nipype.interfaces.dcm2nii import Dcm2niix
import sys
from glob import glob
folder = sys.argv[-1]
files = glob(f"{folder}/*")
print(f"Working on {folder} with {len(files)}")
fromfile = None
convertnode = Node(Dcm2niix(from_file=fromfile), name="convert")
convertnode.base_dir = "/tmp"
convertnode.inputs.source_names = files
convertnode.inputs.out_filename = "/tmp/dcm2niixout%03d" % random.randint(0, 999)
convertnode.terminal_output = "allatonce"
convertnode.inputs.bids_format = True
eg = convertnode.run()
print(f"returncode={eg.runtime.returncode}")which produces
❯ python /tmp/nipype_convert.py /tmp/ttt; echo $?; ls -l /tmp/ttt
Working on /tmp/ttt with 3
230721-10:38:18,884 nipype.workflow INFO:
[Node] Setting-up "convert" in "/tmp/convert".
230721-10:38:18,886 nipype.workflow INFO:
[Node] Outdated cache found for "convert".
230721-10:38:18,888 nipype.workflow INFO:
[Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
230721-10:38:18,918 nipype.interface INFO:
stdout 2023-07-21T10:38:18.918151:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC12.1.0 x86-64 (64-bit Linux)
230721-10:38:18,918 nipype.interface INFO:
stdout 2023-07-21T10:38:18.918151:Found 3 DICOM file(s)
230721-10:38:18,918 nipype.interface INFO:
stdout 2023-07-21T10:38:18.918151:Slices stacked despite coil variation 'H11' vs 'H7' (use '-m o' to turn off merging)
230721-10:38:18,918 nipype.interface INFO:
stdout 2023-07-21T10:38:18.918151:Warning: Interslice distance varies in this volume (incompatible with NIfTI format).
230721-10:38:18,918 nipype.interface INFO:
stdout 2023-07-21T10:38:18.918151:Warning: Missing images? Expected 3 images, but instance number (0020,0013) ranges from 23 to 136
230721-10:38:18,918 nipype.interface INFO:
stdout 2023-07-21T10:38:18.918151:Convert 3 DICOM as ./tmp/dcm2niixout658_cH11_ph (264x288x3x1)
230721-10:38:18,924 nipype.interface INFO:
stdout 2023-07-21T10:38:18.924369:Warning: Unable to rotate 3D volume: slices not equidistant: 40 != 73
230721-10:38:18,924 nipype.interface INFO:
stdout 2023-07-21T10:38:18.924369:Compress: "/usr/bin/pigz" -n -f -6 "./tmp/dcm2niixout658_cH11_ph.nii"
230721-10:38:18,930 nipype.workflow INFO:
[Node] Finished "convert", elapsed time 0.024807s.
returncode=1
0
total 828
-r-------- 1 yoh yoh 282446 Jul 21 10:17 MR.1.3.12.2.1107.5.2.43.167017.2020012914293355999131660
-r-------- 1 yoh yoh 282444 Jul 21 10:17 MR.1.3.12.2.1107.5.2.43.167017.2020012914301930881739443
-r-------- 1 yoh yoh 282440 Jul 21 10:17 MR.1.3.12.2.1107.5.2.43.167017.2020012914320550634554326
so -- it runs, dcm2niix exits with 1, nipype does not fail it, as it does e.g. when dcm2niix exits with 2:
❯ python /tmp/nipype_convert.py /tmp/bogus
Working on /tmp/bogus with 1
230721-10:40:31,406 nipype.workflow INFO:
[Node] Setting-up "convert" in "/tmp/convert".
230721-10:40:31,407 nipype.workflow INFO:
[Node] Outdated cache found for "convert".
230721-10:40:31,409 nipype.workflow INFO:
[Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
230721-10:40:31,439 nipype.interface INFO:
stdout 2023-07-21T10:40:31.439841:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC12.1.0 x86-64 (64-bit Linux)
230721-10:40:31,439 nipype.interface INFO:
stderr 2023-07-21T10:40:31.439955:Error: Unable to find any DICOM images in /tmp/convert (or subfolders 5 deep)
230721-10:40:31,446 nipype.workflow INFO:
[Node] Finished "convert", elapsed time 0.015616s.
230721-10:40:31,446 nipype.workflow WARNING:
[Node] Error on "convert" (/tmp/convert)
Traceback (most recent call last):
File "/tmp/nipype_convert.py", line 18, in <module>
eg = convertnode.run()
^^^^^^^^^^^^^^^^^
File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/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 /tmp/dcm2niixout592 -o . -s n -v n /tmp/convert
Stdout:
Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC12.1.0 x86-64 (64-bit Linux)
Stderr:
Error: Unable to find any DICOM images in /tmp/convert (or subfolders 5 deep)
Traceback:
RuntimeError: subprocess exited with code 2.
Expected behavior
have an exception similar to when exits with code 2
How to replicate the behavior
see above by BYOBD (bring your own broken dicom)
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