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Dear FreeSurfer experts,


I have completed the processes of coregistration of FLAIR to T1 image for the subject. As I ran samseg with lesion contrast, the following error message occurred: 


writing template transform to /home/admin1/freesurfer/subjects/103_samsegOutput/template.lta
writing talairach transform to /home/admin1/freesurfer/subjects/103_samsegOutput/samseg.talairach.lta
atlas registration complete: 0:00:17.614971
/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
  return array(a, dtype, copy=False, order=order)
Traceback (most recent call last):
  File "/home/admin1/freesurfer/python/scripts/run_samseg", line 190, in <module>
    _, _, _, optimizationSummary = samseg.segment(
  File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 255, in segment
    self.preProcess()
  File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 318, in preProcess
    self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages(
  File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/SamsegUtility.py", line 139, in readCroppedImages
    croppedImageBuffers = np.transpose(croppedImageBuffers, axes=[1, 2, 3, 0])
  File "<__array_function__ internals>", line 5, in transpose
  File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 653, in transpose
    return _wrapfunc(a, 'transpose', axes)
  File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 55, in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
  File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 44, in _wrapit
    result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: axes don't match array

Would somebody be kindly advise? Thank you.

Regards,
Krystal

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