ERROR: MultiRegistration::loadMovables: images have different voxel sizes

[chrisgorgo]

ds000114 sub-02

  	 Saving crash info to /output/fmriprep/sub-02/log/20170527-000852_28440498-3e03-4a91-80b9-cf0b460ff9a7/crash-20170527-001301-root-t1_merge-5f63d74f-82be-4e65-ac5b-45abc515530e.pklz
  Interface StructuralReference failed to run. 
  	 Traceback (most recent call last):
    File "/usr/local/miniconda/lib/python3.6/site-packages/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/nipype/pipeline/engine/nodes.py", line 366, in run
      self._run_interface()
  170527-00:13:01,925 workflow INFO:
      self._result = self._run_command(execute)
    File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 607, in _run_command
      result = self._interface.run()
    File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/freesurfer/base.py", line 162, in run
      return super(FSCommand, self).run(**inputs)
    File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base.py", line 1085, in run
      runtime = self._run_wrapper(runtime)
    File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base.py", line 1728, in _run_wrapper
      runtime = self._run_interface(runtime)
    File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base.py", line 1762, in _run_interface
      self.raise_exception(runtime)
    File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base.py", line 1686, in raise_exception
      **runtime.dictcopy()))
  RuntimeError: Command:
  mri_robust_template --satit --fixtp --mov /snapshot/sub-02/ses-retest/anat/sub-02_ses-retest_T1w.nii.gz /snapshot/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz --inittp 1 --iscale --noit --template sub-02_ses-retest_T1w_template.nii.gz --subsample 200
  Standard output:
  $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
  --satit: Will estimate SAT iteratively!
  --fixtp: Will map everything to init TP!
  --mov: Using /snapshot/sub-02/ses-retest/anat/sub-02_ses-retest_T1w.nii.gz as movable/source volume.
  --mov: Using /snapshot/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz as movable/source volume.
      Total: 2 input volumes
  --inittp: Using TP 1 as target for initialization
  --iscale: Enableing intensity scaling!
  --noit: Will output only first template (no iterations)!
  --template: Using sub-02_ses-retest_T1w_template.nii.gz as template output volume.
  --subsample: Will subsample if size is larger than 200 on all axes!
  Setting iscale ...
  reading source '/snapshot/sub-02/ses-retest/anat/sub-02_ses-retest_T1w.nii.gz'...
  converting source '/snapshot/sub-02/ses-retest/anat/sub-02_ses-retest_T1w.nii.gz' to bspline ...
  MRItoBSpline degree 3
  reading source '/snapshot/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz'...
  converting source '/snapshot/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz' to bspline ...
  MRItoBSpline degree 3
  Standard error:
  ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
    Currently not supported, maybe first make conform?
    Debug info: size(1) = 1.2993, 1, 1   size(0) = 1, 1.29978, 1
  MultiRegistration::loadMovables: voxel size is different /snapshot/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz.
  No such file or directory
  Return code: 251

[effigies]

We could add a conform step, or we could check to see whether the two images have the same dimensions and prune the list to a set with uniform dimensions and zooms.

[chrisgorgo]

Some kind of conform would be preferable. We should make sure the final reolution is driven by the input data and not hardcoded (for example 1x1x1).

[effigies]

That makes sense. So let's switch t1_merge and t1_conform, and update t1_conform to take a list of T1w images.

First pass algorithm:

• Reorient all images to RAS
• Take min zoom for each dimension to determine final zooms
• Resample any images that mismatch

It might be worth seeing if there's a tolerance limit in mri_robust_template. I'm not sure it's worth resampling, for example, 1.29978mm to 1.2993mm.

Note that using min zoom will give some pretty weird results if the ratio is too extreme. We could add a check for a max zoom ratio/difference, if that seems like a reasonable thing to check for.