Doesn't quote paths in the invocation of dcm2niix - directory with a space makes execution fail #3604
Description
Summary
Originally reported by a fella co-developer against heudiconv that it crashed when path contained a space in it.
In heudiconv we depend on nipype to just run dcm2niix interface: https://github.com/nipy/heudiconv/blob/master/heudiconv/convert.py#L803
Actual behavior
*(Pdb) p convertnode.inputs anon_bids = <undefined> args = <undefined> bids_format = True comment = <undefined> compress = y compression = <undefined> crop = False environ = {} has_private = False ignore_deriv = <undefined> merge_imgs = False out_filename = sub-b0dwiForFmap_acq-b0dwi_epi_heudiconv133 output_dir = /tmp/tr icky/pytest-of-yoh/pytest-1/test_b0dwi_for_fmap0/sub-b0dwiForFmap/fmap philips_float = <undefined> series_numbers = <undefined> single_file = False source_dir = <undefined> source_names = ['/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00001.dcm', '/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00002.dcm', '/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00003.dcm'] to_nrrd = <undefined> verbose = False observe that output_dir has space in /tmp/tr icky and then running that node kabooms:
(Pdb) convertnode.run() 230915-17:50:37,584 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/tr icky/dcm2niixiftfysju/convert". 230915-17:50:37,588 nipype.workflow INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix> 230915-17:50:37,633 nipype.interface INFO: stdout 2023-09-15T17:50:37.633592:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC13.2.0 x86-64 (64-bit Linux) 230915-17:50:37,633 nipype.interface INFO: stdout 2023-09-15T17:50:37.633592:Warning: only processing last of 2 input files (recompile with 'myEnableMultipleInputs' to recursively process multiple files) 230915-17:50:37,633 nipype.interface INFO: stderr 2023-09-15T17:50:37.633709:Error: Input folder invalid: icky/dcm2niixiftfysju/convert 230915-17:50:37,645 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.020344s. 230915-17:50:37,646 nipype.workflow WARNING: [Node] Error on "convert" (/tmp/tr icky/dcm2niixiftfysju/convert) *** 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-b0dwiForFmap_acq-b0dwi_epi_heudiconv133 -o /tmp/tr icky/pytest-of-yoh/pytest-1/test_b0dwi_for_fmap0/sub-b0dwiForFmap/fmap -s n -v n /tmp/tr icky/dcm2niixiftfysju/convert Stdout: Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC13.2.0 x86-64 (64-bit Linux) Warning: only processing last of 2 input files (recompile with 'myEnableMultipleInputs' to recursively process multiple files) Stderr: Error: Input folder invalid: icky/dcm2niixiftfysju/convert Traceback: RuntimeError: subprocess exited with code 5. (Pdb) import nipype (Pdb) nipype.__version__ '1.8.6' Expected behavior
to not crash
How to replicate the behavior
get heudiconv env, run tests with TMPDIR pointing to a folder with a space in the filename
mkdir /tmp/tr\ icky TMPDIR=/tmp/tr\ icky python -m pytest -s -v heudiconv/tests/test_convert.pyhttps://docs.python.org/3/library/shlex.html#shlex.quote might be of help to quote individual args for POSIX shells if cannot be just passed as a list and shell invocation need to be composed (didn't look what is happening here)