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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
Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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