Hello,
I’m encountering this error when I run the motion correction after generating a mask and segmenting the spinal cord on the DTI sequence, which looks pretty good on QC.
Spinal Cord Toolbox (7.0)
sct_dmri_moco -i 2025-08-17-001_AXIAL_DTI_AND_DIFFUSION_20160515110901_23.nii.gz -m mask_2025-08-17-001_AXIAL_DTI_AND_DIFFUSION_20160515110901_23_dwi_mean.nii.gz -bvec 2025-08-17-001_AXIAL_DTI_AND_DIFFUSION_20160515110901_23.bvec -qc ~/qc_singleSubj -qc-seg dmri_dwi_mean_seg.nii.gz
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Input parameters:
Input file ............ 2025-08-17-001_AXIAL_DTI_AND_DIFFUSION_20160515110901_23.nii.gz
Group size ............ 3
Creating temporary folder (C:\Users\sbaig\AppData\Local\Temp\sct_2025-09-17_19-55-14_moco-wrapper_5ctg4f2p)
Copying input data to tmp folder and convert to nii...
Get dimensions of data...
166 x 66 x 20
Data orientation: RPI
Treated as axial
Set suffix of transformation file name, which depends on the orientation:
Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations
Identify b=0 and DWI images...
WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs.
Transpose bvecs...
Number of b=0: 1 [0]
Number of DWI: 20 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
Split along T dimension...
Merge and average b=0 data...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Merge within groups: 0%| | 0/7 [00:00<?, ?iter/s]Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Merge within groups: 29%|######2 | 2/7 [00:00<00:00, 14.41iter/s]Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Merge within groups: 57%|############5 | 4/7 [00:00<00:00, 10.02iter/s]Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Merge within groups: 86%|##################8 | 6/7 [00:00<00:00, 11.25iter/s]Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Merge within groups: 100%|######################| 7/7 [00:00<00:00, 11.82iter/s]
Merge across groups...
-------------------------------------------------------------------------------
Estimating motion on b=0 images...
-------------------------------------------------------------------------------
Input parameters:
Input file ............ b0.nii
Reference file ........ data_T0000.nii.gz
Polynomial degree ..... 2
Smoothing kernel ...... 1
Gradient step ......... 1
Metric ................ MI
Sampling .............. None
Todo .................. estimate_and_apply
Mask ................. mask.nii
Output mat folder ..... mat_b0groups
Data dimensions:
166 x 66 x 20 x 1
Copy file_target to a temporary file...
Image header specifies datatype 'int32', but array is of type '<class 'numpy.uint8'>'. Header metadata will be overwritten to use '<class 'numpy.uint8'>'.
Register. Loop across Z (note: there is only one Z if orientation is axial)
Z=0/0: 0%| | 0/1 [00:00<?, ?iter/s]
Traceback (most recent call last):
File "C:\Users\sbaig\sct_7.0\spinalcordtoolbox\scripts\sct_dmri_moco.py", line 216, in <module>
main(sys.argv[1:])
File "C:\Users\sbaig\sct_7.0\spinalcordtoolbox\scripts\sct_dmri_moco.py", line 201, in main
fname_output_image = moco_wrapper(param)
File "C:\Users\sbaig\sct_7.0\spinalcordtoolbox\moco.py", line 330, in moco_wrapper
file_mat_b0, _ = moco(param_moco)
File "C:\Users\sbaig\sct_7.0\spinalcordtoolbox\moco.py", line 610, in moco
failed_transfo[it] = register(param, file_data_splitZ_splitT[it], file_target_splitZ[iz], file_mat[iz][it],
File "C:\Users\sbaig\sct_7.0\spinalcordtoolbox\moco.py", line 754, in register
status, output = run_proc(cmd, verbose=1 if param.verbose == 2 else 0, env=env, **kw)
File "C:\Users\sbaig\sct_7.0\spinalcordtoolbox\utils\sys.py", line 334, in run_proc
raise RuntimeError(output)
RuntimeError: setting mask C:\Users\sbaig\AppData\Local\Temp\sct_2025-09-17_19-55-14_moco-wrapper_5ctg4f2p\mask_bin.nii
Exception caught:
itk::ExceptionObject (000000E78519DA60)
Location: "unknown"
File: D:\a\build_ANTs\build_ANTs\antsbin\staging\include\ITK-5.1\itkMattesMutualInformationImageToImageMetricv4.hxx
Line: 312
Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(000002964D39B810): Joint PDF summed to zero
Total runtime; 1.615 seconds.