Using res-2 in output-spaces argument causes failure if a file named "2" exists in the current directory

[stilley2]

This is covered here, but I wanted to document the issue in this repo in case anybody runs into this problem. Effects release 1.4.0.

[oesteban]

Can you provide the stack trace from fMRIPrep? (or a clearer description of how to replicate this)

[stilley2]

Unfortunately fmriprep seems to catch and disregard the stack trace somehow (I never tracked down how), but here's the end of the log. The error occurs because I have a fail named "2" in my home directory.

 [Node] Setting-up "fmriprep_wf.single_subject_YYYY_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/mnt/work/fmriprep_wf/single_subject_YYYY
_wf/anat_preproc_wf/anat_norm_wf/outputnode".
190608-08:41:53,852 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_wf.single_subject_YYYY_wf.anat_preproc_wf.anat_derivatives_wf.lut_tpl_seg" in "/mnt/work/fmriprep_wf/single_subject_
YYYY_wf/anat_preproc_wf/anat_derivatives_wf/_template_MNI152NLin6Asym/lut_tpl_seg".
190608-08:41:53,854 nipype.workflow INFO:
         [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface")
190608-08:41:53,855 nipype.workflow INFO:
         [Node] Running "lut_tpl_seg" ("nipype.interfaces.utility.wrappers.Function")
190608-08:41:53,862 nipype.workflow INFO:
         [Node] Finished "fmriprep_wf.single_subject_YYYY_wf.anat_preproc_wf.anat_norm_wf.outputnode".
190608-08:41:54,61 nipype.workflow INFO:
         [Node] Finished "fmriprep_wf.single_subject_YYYY_wf.anat_preproc_wf.anat_derivatives_wf.lut_tpl_seg".
fMRIPrep failed: File /mnt/work/fmriprep_wf/single_subject_YYYY_wf/func_preproc_task_face_wf/bold_std_trans_wf/_key_MNI152NLin6Asym/select_std/2 not foun
d
190608-08:42:04,458 nipype.workflow INFO:
         [Node] Finished "fmriprep_wf.single_subject_XXXX_wf.anat_preproc_wf.t1_seg".
190608-08:43:54,132 nipype.workflow INFO:
         [Node] Finished "_autorecon30".
190608-08:44:32,980 nipype.workflow INFO:
         [Node] Finished "_autorecon31".
190608-08:45:23,538 nipype.workflow INFO:
         [Node] Finished "_autorecon30".
190608-08:50:29,280 nipype.workflow INFO:
         [Node] Finished "_autorecon_surfs0".
190608-08:50:48,482 nipype.workflow INFO:
         [Node] Finished "_autorecon_surfs0".
190608-08:52:51,245 nipype.workflow INFO:
         [Node] Finished "_midthickness0".
190608-08:53:58,810 nipype.workflow INFO:
         [Node] Finished "_midthickness1".
190608-08:54:07,365 nipype.workflow INFO:
         [Node] Finished "_autorecon30".
190608-08:54:55,872 nipype.workflow INFO:
         [Node] Finished "_autorecon31".
190608-09:07:59,851 nipype.workflow INFO:
         [Node] Finished "fmriprep_wf.single_subject_XXXX_wf.anat_preproc_wf.anat_norm_wf.registration".
190608-09:12:37,347 nipype.workflow INFO:
         [Node] Finished "_autorecon_surfs1".
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))

[oesteban]

What is the exact command line you are running? Are you using docker or any other container?