🐛 convert_motionxfm2itk_188: c3d_affine_tool […] died with <Signals.SIGABRT: 6>

[shnizzedy]

Describe the bug

Node: cpac_sub-colornest035_ses-1.convert_motionxfm2itk_188
Working directory: /outputs/working/cpac_sub-colornest035_ses-1/_scan_rest_run-01/convert_motionxfm2itk_188

Node inputs:

function_str = def run_c3d(reference_file, source_file, transform_file):

    import os
    import subprocess

    itk_transform = os.path.join(os.getcwd(), 'affine.txt')

    cmd = ['c3d_affine_tool', '-ref', reference_file, '-src',
            source_file, transform_file, '-fsl2ras', '-oitk', itk_transform]
    retcode = subprocess.check_output(cmd)

    return itk_transform

reference_file = <undefined>
source_file = <undefined>
transform_file = ['/outputs/working/cpac_sub-colornest035_ses-1/_scan_rest_run-01/oned_matrix_concat_86/MD5E-s43982431--4505293d1740413480db269995b35cf6_calc.aff12.1D']

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/code/CPAC/pipeline/nipype_pipeline_engine/engine.py", line 388, in run
    return super().run(updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1386, in _run_interface
    self.config["execution"]["stop_on_first_crash"]
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1295, in _collate_results
    "Subnodes of node: %s failed:\n%s" % (self.name, "\n".join(msg))
Exception: Subnodes of node: convert_motionxfm2itk_188 failed:
Subnode 0 failed
Error: Traceback (most recent call last):

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 94, in nodelist_runner
    result = node.run(updatehash=updatehash)

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
    runtime = self._run_interface(runtime)

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
    out = function_handle(**args)

  File "<string>", line 10, in run_c3d

  File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout

  File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)

subprocess.CalledProcessError: Command '['c3d_affine_tool', '-ref', '/outputs/working/cpac_sub-colornest035_ses-1/_scan_rest_run-01/func_get_fmriprep_ref_83/ref_bold.nii.gz', '-src', '/outputs/working/cpac_sub-colornest035_ses-1/_scan_rest_run-01/func_get_fmriprep_ref_83/ref_bold.nii.gz', '/outputs/working/cpac_sub-colornest035_ses-1/_scan_rest_run-01/oned_matrix_concat_86/MD5E-s43982431--4505293d1740413480db269995b35cf6_calc.aff12.1D', '-fsl2ras', '-oitk', '/outputs/working/cpac_sub-colornest035_ses-1/_scan_rest_run-01/convert_motionxfm2itk_188/mapflow/_convert_motionxfm2itk_1880/affine.txt']' died with <Signals.SIGABRT: 6>.

Running the command in a container:

terminate called after throwing an instance of 'char const*'

To reproduce

Run with

functional_preproc:
  motion_estimates_and_correction:
    motion_correction:
      using: [3dvolreg]
registration_workflows: 
  functional_registration:
    func_registration_to_template:
      apply_transform:
        using: single_step_resampling

Expected behavior

c3d_affine_tool succeeds

Acceptance criteria

• c3d_affine_tool succeeds
  or
• 'single_step_resampling' is explicitly disallowed for 3dvolreg

Screenshots

No response

C-PAC version

v1.8.4-dev

Container platform

Singularity

Docker and/or Singularity version(s)

Singularity 3.8.5-2.el7

Additional context

No response

[shnizzedy]

mcflirt

*.mat directory with 150 MAT_* files, each 4 × 4

3dvolreg

*.1D file with shape 152 × 12

[shnizzedy]

The diagonals in the MAT_* files are 1s

[gkiar]

What about the right column or the bottom row? Are they predominantly 0s?

[shnizzedy]

the bottom rows are all 0 0 0 1

[gkiar]

Perfect. As discussed over Slack, the solution then is to reshape each 1 x 12 row into 3 x 4 and pad it with 0 0 0 1 to conform to the homogeneous coordinates standard.

[shnizzedy]

That did the trick!

C-PAC/CPAC/registration/utils.py

Lines 501 to 531 in 10f1d4d

	def one_d_to_mat(one_d_filename):
	"""Convert a .1D file to a .mat directory
	Parameters
	----------
	one_d_filename : str
	The filename of the .1D file to convert
	Returns
	-------
	mat_filenames : list of str
	The of paths in the .mat directory created
	"""
	mat_dirname = one_d_filename.replace('.1D', '.mat')
	with open(one_d_filename, 'r') as one_d_file:
	rows = [np.reshape(row, (4, 4)).astype('float') for row in [[
	term.strip() for term in row.split(' ') if term.strip()
	] + [0, 0, 0, 1] for row in [
	line.strip() for line in one_d_file.readlines() if
	not line.startswith('#')]]]
	try:
	os.mkdir(mat_dirname)
	except FileExistsError:
	pass
	for i, row in enumerate(rows):
	np.savetxt(os.path.join(mat_dirname, f'MAT_{i:04}'),
	row, fmt='%.5f', delimiter=' ')
	mat_filenames = [os.path.join(mat_dirname, filename) for
	filename in os.listdir(mat_dirname)]
	mat_filenames.sort()
	return mat_filenames

C-PAC/CPAC/registration/registration.py

Lines 3752 to 3766 in 10f1d4d

	motion_correct_tool = cfg['functional_preproc',
	'motion_estimates_and_correction',
	'motion_correction', 'using']
	if motion_correct_tool == 'mcflirt':
	wf.connect(node, out, motionxfm2itk, 'transform_file')
	elif motion_correct_tool == '3dvolreg':
	convert_transform = pe.Node(util.Function(
	input_names=['one_d_filename'],
	output_names=['transform_directory'],
	function=one_d_to_mat,
	imports=['import os', 'import numpy as np']),
	name=f'convert_transform_{pipe_num}')
	wf.connect(node, out, convert_transform, 'one_d_filename')
	wf.connect(convert_transform, 'transform_directory',
	motionxfm2itk, 'transform_file')