Paranoia/fmriprep/sub-tb3784/log/20190204-211754_397d56c2-c280-471b-ac54-42e2a3623950/crash-20190205-022004-delavega-flt_bbr-dfb1f6f7-6edf-4c14-b0ab-df194db827a5.txt

Node: fmriprep_wf.single_subject_tb3784_wf.func_preproc_task_story3_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr
Working directory: /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/func_preproc_task_story3_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr

Node inputs:

angle_rep = <undefined>
apply_isoxfm = <undefined>
apply_xfm = <undefined>
args = <undefined>
bbrslope = <undefined>
bbrtype = <undefined>
bgvalue = <undefined>
bins = <undefined>
coarse_search = <undefined>
compress_report = auto
cost = <undefined>
cost_func = bbr
datatype = <undefined>
display_init = <undefined>
dof = 6
echospacing = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
fieldmap = <undefined>
fieldmapmask = <undefined>
fine_search = <undefined>
force_scaling = <undefined>
in_file = /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/func_preproc_task_story3_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
in_matrix_file = /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/func_preproc_task_story3_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr_init/uni_xform_masked_flirt.mat
in_weight = <undefined>
interp = <undefined>
min_sampling = <undefined>
no_clamp = <undefined>
no_resample = <undefined>
no_resample_blur = <undefined>
no_search = <undefined>
out_file = <undefined>
out_log = <undefined>
out_matrix_file = <undefined>
out_report = report.svg
output_type = NIFTI_GZ
padding_size = <undefined>
pedir = <undefined>
ref_weight = <undefined>
reference = /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_BrainExtractionBrain.nii.gz
rigid2D = <undefined>
save_log = <undefined>
schedule = /usr/share/fsl/5.0/etc/flirtsch/bbr.sch
searchr_x = <undefined>
searchr_y = <undefined>
searchr_z = <undefined>
sinc_width = <undefined>
sinc_window = <undefined>
uses_qform = <undefined>
verbose = <undefined>
wm_seg = /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_wm.nii.gz
wmcoords = <undefined>
wmnorms = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 369, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 689, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
flirt -in /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/func_preproc_task_story3_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz -ref /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_BrainExtractionBrain.nii.gz -out uni_xform_masked_flirt.nii.gz -omat uni_xform_masked_flirt.mat -searchcost bbr -dof 6 -init /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/func_preproc_task_story3_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr_init/uni_xform_masked_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_wm.nii.gz
Standard output:

Standard error:
** ERROR (nifti_image_read): short header read '/work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_wm.nii.gz'
** ERROR: nifti_image_open(/work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_wm): bad header info
ERROR: failed to open file /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_wm
Image Exception : #22 :: ERROR: Could not open image /work/04578/delavega/lonestar/fmriprep/work/fmriprep_wf/single_subject_tb3784_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_wm
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
Return code: 134