Fmriprep: syn_i and syn_j crash when using --syn-sdc

[Gilles86]

When I use the --syn-sdc on one of my datasets, I get the following error for all the run of one out of 9 subjects (the rest finishes without errors):

Node: fmriprep_wf.single_subject_02_wf.func_preproc_task_binocularrivalry_run_01_wf.nonlinear_sdc_wf.syn_i
Working directory: /scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/syn_i

Node inputs:

args = <undefined>
collapse_output_transforms = True
convergence_threshold = [1e-08, 1e-08]
convergence_window_size = [20, 10]
dimension = 3
environ = {'NSLOTS': '1'}
fixed_image = ['/scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/t1_2_ref/highres001_BrainExtractionBrain_inv_trans.nii.gz']
fixed_image_mask = <undefined>
fixed_image_masks = ['NULL', '/scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/threshold_atlas/fmap_atlas_trans_maths.nii.gz']
float = True
ignore_exception = False
initial_moving_transform = <undefined>
initial_moving_transform_com = <undefined>
initialize_transforms_per_stage = False
interpolation = Linear
interpolation_parameters = <undefined>
invert_initial_moving_transform = <undefined>
metric = ['Mattes', 'CC']
metric_item_trait = <undefined>
metric_stage_trait = <undefined>
metric_weight = [1.0, 1.0]
metric_weight_item_trait = <undefined>
metric_weight_stage_trait = <undefined>
moving_image = ['/scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/bold_hmc_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_masked.nii.gz']
moving_image_mask = <undefined>
moving_image_masks = <undefined>
num_threads = 1
number_of_iterations = [[100, 50], [20, 10]]
output_inverse_warped_image = <undefined>
output_transform_prefix = ants_susceptibility
output_warped_image = True
radius_bins_item_trait = <undefined>
radius_bins_stage_trait = <undefined>
radius_or_number_of_bins = [56, 5]
restore_state = <undefined>
restrict_deformation = [[1, 0, 0], [1, 0, 0]]
sampling_percentage = <undefined>
sampling_percentage_item_trait = <undefined>
sampling_percentage_stage_trait = <undefined>
sampling_strategy = <undefined>
sampling_strategy_item_trait = <undefined>
sampling_strategy_stage_trait = <undefined>
save_state = <undefined>
shrink_factors = [[2, 1], [1, 1]]
sigma_units = ['vox', 'vox']
smoothing_sigmas = [[1.0, 0.0], [1.0, 0.0]]
terminal_output = stream
transform_parameters = [(0.8, 2.0, 2.0), (0.8, 2.0, 2.0)]
transforms = ['SyN', 'SyN']
use_estimate_learning_rate_once = [True, True]
use_histogram_matching = [True, True]
verbose = <undefined>
winsorize_lower_quantile = 0.001
winsorize_upper_quantile = 1.0
write_composite_transform = False

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 52, 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 372, in run
    self._run_interface()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 482, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 613, in _run_command
    result = self._interface.run()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1083, in run
    runtime = self._run_wrapper(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1757, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1791, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1715, in raise_exception
    **runtime.dictcopy()))
RuntimeError: Command:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation Linear --output [ ants_susceptibility, ants_susceptibility_Warped.nii.gz ] --transform SyN[ 0.8, 2.0, 2.0 ] --metric Mattes[ /scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/t1_2_ref/highres001_BrainExtractionBrain_inv_trans.nii.gz, /scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/bold_hmc_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_masked.nii.gz, 1, 56 ] --convergence [ 100x50, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --restrict-deformation 1x0x0 --masks [ NULL, NULL ] --transform SyN[ 0.8, 2.0, 2.0 ] --metric CC[ /scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/t1_2_ref/highres001_BrainExtractionBrain_inv_trans.nii.gz, /scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/bold_hmc_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_masked.nii.gz, 1, 5 ] --convergence [ 20x10, 1e-08, 10 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 1x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --restrict-deformation 1x0x0 --masks [ /scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/threshold_atlas/fmap_atlas_trans_maths.nii.gz, NULL ] --winsorize-image-intensities [ 0.001, 1.0 ]  --write-composite-transform 0
Standard output:

Standard error:
 file NULL does not exist . 
 file NULL does not exist . 
 file NULL does not exist . 
/tmp/ANTs/build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (2) from SVDC
/tmp/ANTs/build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 2x2
M = [ ...
            -nan             -nan 
            -nan             -nan  ]

Return code: 1
Interface Registration failed to run. 

[effigies]

You're running in Singularity? I wonder if there's a conflicting version of ANTs in your environment. Singularity does a kind of minimal masking of the environment, so it's possible that the native installation of ANTs is being run instead of the version in the container.

[Gilles86]

I'm running under Singularity, but I have no ANTS binaries in my PATH. I sent you an email with the data, so you can maybe have a look if you have time.

[oesteban]

@effigies is that 'NULL' in

fixed_image_masks = ['NULL', '/scratch/wf/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/threshold_atlas/fmap_atlas_trans_maths.nii.gz']

acceptable?

• seems like ANTs is trying to open a file named NULL...

[chrisgorgo]

Weird I never got the email from you @Gilles86

[effigies]

@oesteban That's expected (and actually hard-coded), but pre-2.2.0 it would have caused issues. That's why I at first thought that the wrong version of ANTs might be being called.

[effigies]

I was able to reproduce this issue with the provided data.

[effigies]

This seems to be another partial FoV issue. The ref_2_t1 node is producing the identity affine:

Transform file: /data/scratch/hollander/fmriprep_wf/single_subject_02_wf/func_preproc_task_binocularrivalry_run_01_wf/nonlinear_sdc_wf/ref_2_t1/transform0GenericAffine.mat
AffineTransform (0x2d83e00)
  RTTI typeinfo:   itk::AffineTransform<double, 3u>
  Reference Count: 3
  Modified Time: 660
  Debug: Off
  Object Name: 
  Observers: 
    none
  Matrix: 
    1 0 0 
    0 1 0 
    0 0 1 
  Offset: [0, 0, 0]
  Center: [0, 0, 0]
  Translation: [0, 0, 0]
  Inverse: 
    1 0 0 
    0 1 0 
    0 0 1 
  Singular: 0

I suspect the initial transform is failing to overlap.