FSL FUGUE - Image Exception : #3 :: Attempted to divide images/ROIs of different sizes

[tragus1]

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
    load_entry_point('fmriprep==1.0.8', 'console_scripts', 'fmriprep')()
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 267, in main
    fmriprep_wf.run(**plugin_settings)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 168, in run
    self._clean_queue(jobid, graph, result=result))
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
    raise RuntimeError("".join(result['traceback']))
RuntimeError: 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/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:
fugue --despike --despikethreshold=2.1 --loadfmap=/root/src/fmriprep/work/fmriprep_wf/single_subject_ACTIGLIA011BL_wf/func_preproc_task_rest_wf/phdiff_wf/demean/sub-ACTIGLIA011BL_acq-rest_phasediff_rads_unwrapped_filt_demean.nii.gz --savefmap=sub-ACTIGLIA011BL_acq-rest_phasediff_rads_unwrapped_filt_demean_fieldmap.nii.gz --mask=/root/src/fmriprep/work/fmriprep_wf/single_subject_ACTIGLIA011BL_wf/func_preproc_task_rest_wf/phdiff_wf/bet/sub-ACTIGLIA011BL_acq-rest_magnitude1_ras_corrected_brain_mask.nii.gz
Standard output:

Standard error:
Image Exception : poldracklab/fmriprep#3 :: Attempted to divide images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
Return code: 134

[oesteban]

Could you share some data to replicate this?

[tragus1]

Thank you very much. I´ve sent you an email with the link to the download of the data.
Best regards
Boris

[effigies]

Hi @tragus1 can you verify that this issue persists in the most recent release of fMRIPrep (1.3.0.post2)?

[dorianps]

I found this thread while searching for a similar error from some of our subjects. I would understand if this is a field map issue because we have some other problems with Philips fieldmaps. The question is: how do we know what is the source of the problem, and what could be a solution?

Here is the crash log:

Node: fmriprep_wf.single_subject_S12345678_wf.func_preproc_ses_07_task_restingstate_run_01_wf.sdc_estimate_wf.phdiff_wf.fmap_postproc_wf.cleanup_wf.Despike
Working directory: /DATA/dorian/fmriprepdata/STUDY/data/processed/fmriprep-1.5.5/work_sub-S12345678/fmriprep_wf/single_subject_S12345678_wf/func_preproc_ses_07_task_restingstate_run_01_wf/sdc_estimate_wf/phdiff_wf/fmap_postproc_wf/cleanup_wf/Despike

Node inputs:

args = <undefined>
asym_se_time = <undefined>
despike_2dfilter = True
despike_threshold = 2.1
dwell_time = <undefined>
dwell_to_asym_ratio = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
fmap_in_file = <undefined>
fmap_out_file = <undefined>
forward_warping = False
fourier_order = <undefined>
icorr = <undefined>
icorr_only = <undefined>
in_file = <undefined>
mask_file = <undefined>
median_2dfilter = <undefined>
no_extend = <undefined>
no_gap_fill = <undefined>
nokspace = <undefined>
output_type = NIFTI_GZ
pava = <undefined>
phase_conjugate = <undefined>
phasemap_in_file = <undefined>
poly_order = <undefined>
save_fmap = True
save_shift = <undefined>
save_unmasked_fmap = <undefined>
save_unmasked_shift = <undefined>
shift_in_file = <undefined>
shift_out_file = <undefined>
smooth2d = <undefined>
smooth3d = <undefined>
unwarp_direction = <undefined>
unwarped_file = <undefined>
warped_file = <undefined>

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 "/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 397, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 792, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 723, in raise_exception
    ).format(**runtime.dictcopy())
RuntimeError: Command:
fugue --despike --despikethreshold=2.1 --loadfmap=/DATA/dorian/fmriprepdata/STUDY/data/processed/fmriprep-1.5.5/work_sub-S12345678/fmriprep_wf/single_subject_S12345678_wf/func_preproc_ses_07_task_restingstate_run_01_wf/sdc_estimate_wf/phdiff_wf/fmap_postproc_wf/demean/sub-S12345678_ses-07_run-03_phasediff_rads_unwrapped_recentered_filt_demean.nii.gz --savefmap=sub-S12345678_ses-07_run-03_phasediff_rads_unwrapped_recentered_filt_demean_fieldmap.nii.gz --mask=/DATA/dorian/fmriprepdata/STUDY/data/processed/fmriprep-1.5.5/work_sub-S12345678/fmriprep_wf/single_subject_S12345678_wf/func_preproc_ses_07_task_restingstate_run_01_wf/sdc_estimate_wf/phdiff_wf/magnitude_wf/bet/sub-S12345678_ses-07_run-03_magnitude1_avg_corrected_brain_mask.nii.gz
Standard output:

Standard error:
Image Exception : #3 :: Attempted to divide images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
Return code: 134

[oesteban]

Hi @dorianps, could you confirm whether the dimensions of the magnitude file match those of the phase difference?

[ins0mniac2]

The dimensions are the same.

[ins0mniac2]

@oesteban : I looked at the files further. Even though the dimensions of the original magnitude and phase difference files match, the two input files to the fugue command that threw the error have "different" sizes. I put that in quotes because the difference is in orientation, they do have the same size along the anatomical axes. See below c3d output:

func_preproc_ses_07_task_restingstate_run_01_wf/sdc_estimate_wf/phdiff_wf/fmap_postproc_wf/demean/sub-12345_ses-07_run-03_phasediff_rads_unwrapped_recentered_filt_demean.nii.gz -info
Image #1: dim = [64, 64, 48]; bb = {[77.644 -116.206 -94.8365], [289.644 95.7936 63.7555]}; vox = [3.3125, 3.3125, 3.304]; range = [-4.02648, 5.25277]; orient = AIL

and

func_preproc_ses_07_task_restingstate_run_01_wf/sdc_estimate_wf/phdiff_wf/magnitude_wf/bet/sub-12345_ses-07_run-03_magnitude1_avg_corrected_brain_mask.nii.gz -info
Image #1: dim = [48, 64, 64]; bb = {[77.644 92.4811 -94.8365], [236.236 304.481 117.164]}; vox = [3.304, 3.3125, 3.3125]; range = [0, 1]; orient = LPI

[dorianps]

@oesteban We are still stuck with this problem. Any suggestion of how to figure out what might be the problem? Note, this happens with fmriprep 1.5.X, we have processed the rest of the data with that version and are hoping not to need 20.0.X just for 3 subjects.

Thank you for helping out.

[effigies]

To be clear, the original fieldmaps have a common orientation, but they've been changed by the time they get to demean/bet? Or we're failing to normalize to correct orientations?