Skullstripping Error using MRIQC with Docker

Hello,

I am a newbie to to Docker and MRIQC. My data is in BIDS format and I’m able to run MRIQC without any glitches on 10 test images, but when I run it on my dataset of 100 images, I get a skullstripping crashlog which I have pasted below.

I’d be grateful for any suggestions.

Khushboo.

Node: workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip
Working directory: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-HU3215…anat…sub-HU3215_T1w.nii/skullstrip

Node inputs:

args =
environ = {}
ignore_exception = False
in_file = /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-HU3215…anat…sub-HU3215_T1w.nii/inu_n4/sub-HU3215_T1w_conformed_corrected.nii
num_threads = 1
out_file =
outputtype = NIFTI_GZ
terminal_output =

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 487, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 571, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 650, 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 516, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/afni/base.py”, line 110, in _run_interface
return super(AFNICommandBase, self)._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 1023, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 960, in raise_exception
).format(*runtime.dictcopy()))
RuntimeError: Command:
3dSkullStrip -input /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-HU3215…anat…sub-HU3215_T1w.nii/skullstrip/sub-HU3215_T1w_conformed_corrected.nii -prefix sub-HU3215_T1w_conformed_corrected_skullstrip.nii.gz
Standard output:
** Memory usage: chunks=189 bytes=100124972
Standard error:
e[7m
+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-HU3215…anat…sub-HU3215_T1w.nii/skullstrip/sub-HU3215_T1w_conformed_corrected.nii,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-HU3215…anat…sub-HU3215_T1w.nii/skullstrip/sub-HU3215_T1w_conformed_corrected.nii is 15.427585 degrees from plumb.

Fatal Signal 11 (SIGSEGV) received
SUMA_SurfGridIntersect
SUMA_FindVoxelsInSurface
3dSkullStrip
Bottom of Debug Stack
** AFNI version = AFNI_17.3.03 Compile date = Nov 9 2017
** [[Precompiled binary linux_ubuntu_16_64: Nov 9 2017]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /root/.afni.crashlog
Return code: 1

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