Fmriprep itk::error during brain extraction

ants
fmriprep
#1

Hi,

I am preprocessing a dataset of 170 subjects with fmriprep and the processing stops during the brain extraction. Can you help me figuring out what the problem is?

I attached crash log from an example participant.

I am using the version 1.3.2 and I´ve copied the specs for the file and the command from the html:

Summary

  • Subject ID: 109
  • Structural images: 1 T1-weighted
  • Functional series: 1
    • Task: rest (1 run)
  • Resampling targets: fsaverage5, MNI152NLin2009cAsym
  • FreeSurfer reconstruction: Run by fMRIPrep

Anatomical

Anatomical Conformation

  • Input T1w images: 1
  • Output orientation: RAS
  • Output dimensions: 240x320x320
  • Output voxel size: 0.85mm x 0.85mm x 0.85mm
  • Discarded images: 0

Functional

Note on orientation: qform matrix overwritten

The qform has been copied from sform.

About

  • FMRIPrep version: 1.3.2
  • FMRIPrep command: /usr/local/miniconda/bin/fmriprep /data/pt_02147/BIDS/ /data/pt_02147/BIDS_OUT/ --template MNI152NLin2009cAsym --template-resampling-grid /data/pt_02147/MNI152_T1_2mm.nii.gz --no-submm-recon --fs-license-file /data/pt_02147/prep/license.txt -w /data/pt_02147/BIDS_WD/ participant --participant-label 109
  • Date preprocessed: 2019-04-09 08:57:14 +0000

Errors

  • Node Name: fmriprep_wf.single_subject_109_wf.anat_preproc_wf.brain_extraction_wf.init_aff

crash-20190409-090353-lauckner-init_aff-5f5a8b29-efe6-4d50-9c98-4234b16d9b79.txt (3.1 KB)

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#2

Can you check that the original file is actually not empty?

/data/pt_02147/BIDS/sub-109/anat/sub-109_T1w.nii.gz
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#3

Hi,

I can confirm, that this file is not empty. All structural files are stopped with the same error.

A little piece of extra information. The dimensionality of these structural images is unusually high and I ran into errors previously because of a high FOV, which I was able to circumvent using the --no-submm-reconoption. But now there is this problem. Could the FOV be the problem here? It would be an easy step to crop the dimensionality.

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#4

Could you share that image with me?

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