Fmriprep error in antsBRainExtraction: Segmentation fault +T1w.nii.gz does not exist (it does + dataset passes BIDS validation)

brai · July 25, 2018, 1:33pm

Dear fmriprep team,

Would appreciate your help with the following error:

180725-10:05:26,986 workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_022_wf.func_preproc_task_stroopst_wf.bold_hmc_wf.fsl2itk” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/func_preproc_task_stroopst_wf/bold_hmc_wf/fsl2itk”.
180725-10:05:26,993 workflow INFO:
[Node] Running “fsl2itk” (“fmriprep.interfaces.itk.MCFLIRT2ITK”)
180725-10:05:36,427 workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_022_wf.func_preproc_task_stroopst_wf.bold_hmc_wf.fsl2itk”.
180725-10:05:38,218 workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_022_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip”.
180725-10:05:38,221 workflow INFO:
[Node] Running “t1_skull_strip” (“niworkflows.nipype.interfaces.ants.segmentation.BrainExtraction”), a CommandLine Interface with command:
antsBrainExtraction.sh -a /data/sub-022/anat/sub-022_T1w.nii.gz -m /root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz -d 3 -f /niworkflows_data/ants_oasis_template_ras/T_template0_BrainCerebellumRegistrationMask.nii.gz -s nii.gz -k 1 -o highres001_ -q 1
180725-10:37:40,934 workflow WARNING:
[Node] Error on “fmriprep_wf.single_subject_022_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip” (/root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip)
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
load_entry_point(‘fmriprep==1.0.12’, ‘console_scripts’, ‘fmriprep’)()
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 314, in main
fmriprep_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py”, line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py”, line 168, in run
self._clean_queue(jobid, graph, result=result))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py”, line 227, in _clean_queue
raise RuntimeError("".join(result[‘traceback’]))
RuntimeError: Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py”, line 68, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 480, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 564, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 644, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 520, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/ants/segmentation.py”, line 828, in _run_interface
runtime = super(BrainExtraction, self)._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 1020, in run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 957, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
antsBrainExtraction.sh -a /data/sub-022/anat/sub-022_T1w.nii.gz -m /root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz -d 3 -f /niworkflows_data/ants_oasis_template_ras/T_template0_BrainCerebellumRegistrationMask.nii.gz -s nii.gz -k 1 -o highres001 -q 1
Standard output:

Will run Atropos segmentation with K=3. Classes labeled in order of mean intensity. Assuming CSF=1, GM=2, WM=3

The output directory “highres001_” does not exist. Making it.
--------------------- Running antsBrainExtraction.sh on ce672c13d2e8 ---------------------

Bias correction of anatomical images (pre brain extraction)

pre-process by truncating the image intensities

run N4

BEGIN >>>>>>>>>>>>>>>>>>>>
/usr/lib/ants/ImageMath 3 highres001_N4Truncated0.nii.gz TruncateImageIntensity /data/sub-022/anat/sub-022_T1w.nii.gz 0.01 0.999 256
END <<<<<<<<<<<<<<<<<<<<

BEGIN >>>>>>>>>>>>>>>>>>>>
/usr/lib/ants/N4BiasFieldCorrection -d 3 -i highres001_N4Truncated0.nii.gz -s 4 -c [50x50x50x50,0.0000001] -b [200] -o highres001_N4Corrected0.nii.gz --verbose 1

Running N4 for 3-dimensional images.

Mask not read. Using the entire image as the mask.

Specified spline distance: 200mm
original image size: [256, 256, 192]
padded image size: [401, 401, 201]
number of control points: [5, 5, 4]

Current level = 1
Iteration 1 (of 50). Current convergence value = 0.000266834 (threshold = 1e-07)
Iteration 2 (of 50). Current convergence value = 0.000200864 (threshold = 1e-07)
Iteration 3 (of 50). Current convergence value = 0.000156018 (threshold = 1e-07)
.
.
.

2DIAGNOSTIC, 100, -5.814228653908e-01, 3.172523577177e-07, 3.4243e+02, 1.9823e+00,
Elapsed time (stage 0): 3.4453e+02

Stage 1
iterations = 1000x500x250x100
convergence threshold = 1.0000e-08
convergence window size = 10
number of levels = 4
using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
preprocessing: winsorizing the image intensities
preprocessing: histogram matching the images
Shrink factors (level 1 out of 4): [8, 8, 8]
Shrink factors (level 2 out of 4): [4, 4, 4]
Shrink factors (level 3 out of 4): [2, 2, 2]
Shrink factors (level 4 out of 4): [1, 1, 1]
smoothing sigmas per level: [4, 2, 1, 0]
regular sampling (percentage = 2.5000e-01)

*** Running AffineTransform registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
2DIAGNOSTIC, 1, -1.042005896568e+00, inf, 6.4135e+00, 6.4135e+00,
.
.
.
1DIAGNOSTIC, 8, -6.264878511429e-01, inf, 8.3084e+02, 5.6771e+01,
1DIAGNOSTIC, 9, -6.291846036911e-01, inf, 8.9057e+02, 5.9736e+01,
1DIAGNOSTIC, 10, -6.317657232285e-01, inf, 9.4843e+02, 5.7858e+01,
Elapsed time (stage 2): 960.6

Total elapsed time: 1755
END <<<<<<<<<<<<<<<<<<<<

BEGIN >>>>>>>>>>>>>>>>>>>>
/usr/lib/ants/antsApplyTransforms -d 3 -i /root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -o highres001_BrainExtractionPriorWarped.nii.gz -r /data/sub-022/anat/sub-022_T1w.nii.gz -n Gaussian -t [highres001_BrainExtractionPrior0GenericAffine.mat,1] -t highres001_BrainExtractionPrior1InverseWarp.nii.gz --float 1 --verbose 1
Using single precision for computations.
Input scalar image: /root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz
Reference image: /data/sub-022/anat/sub-022_T1w.nii.gz

The composite transform comprises the following transforms (in order):

highres001_BrainExtractionPrior1InverseWarp.nii.gz (type = DisplacementFieldTransform)

inverse of highres001_BrainExtractionPrior0GenericAffine.mat (type = AffineTransform)
=============================================================================
Default pixel value: 0
ERROR: command exited with nonzero status 139
Command: /usr/lib/ants/antsApplyTransforms -d 3 -i /root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -o highres001_BrainExtractionPriorWarped.nii.gz -r /data/sub-022/anat/sub-022_T1w.nii.gz -n Gaussian -t [highres001_BrainExtractionPrior0GenericAffine.mat,1] -t highres001_BrainExtractionPrior1InverseWarp.nii.gz --float 1 --verbose 1

Standard error:
Using antsBrainExtraction with the following arguments:
  image dimension         = 3
  anatomical image        = /data/sub-022/anat/sub-022_T1w.nii.gz
  extraction template     = /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz
  extraction reg. mask    = /niworkflows_data/ants_oasis_template_ras/T_template0_BrainCerebellumRegistrationMask.nii.gz
  extraction prior        = /root/src/fmriprep/work/fmriprep_wf/single_subject_022_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz
  output prefix           = highres001_
  output image suffix     = nii.gz

N4 parameters (pre brain extraction):
  convergence             = [50x50x50x50,0.0000001]
  shrink factor           = 4
  B-spline parameters     = [200]

Atropos parameters (extraction):
   convergence            = [3,0.0]
   likelihood             = Gaussian
   initialization         = kmeans[3]
   mrf                    = [0.1,1x1x1]
   use clock random seed  = 1
file /data/sub-022/anat/sub-022_T1w.nii.gz does not exist .
/usr/lib/ants/antsBrainExtraction.sh: line 117: 20470 Segmentation fault $cmd
Return code: 1

ChrisGorgolewski · July 25, 2018, 2:14pm

The key error here is segmentation fault. You are most likely running out of memory. If you are using docker check the settings to make sure you expose enough RAM.