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Hi!
I'm trying to run recon-all-clinical but I'm running into an error with the
SynthSeg at the very beginning. Do you have any hints what the problem
might be here? Here's the full error message:
the following problem occured with image [mypath]/mri/native.mgz :
Traceback (most recent call last):
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in
predict
image, aff, h, im_res, shape, pad_idx, crop_idx =
preprocess(path_image=path_images[i],
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in
preprocess
im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image,
True)
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in
get_volume_info
im, aff, header = load_volume(path_volume, im_only=False)
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in
load_volume
x = nib.load(path_volume)
File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/loadsave.py",
line 110, in load
img = image_klass.from_filename(filename, **kwargs)
File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
line 503, in from_filename
return klass.from_file_map(file_map, mmap=mmap,
keep_file_open=keep_file_open)
File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
line 526, in from_file_map
header = klass.header_class.from_fileobj(mghf)
File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
line 171, in from_fileobj
+ int(klass._data_type_codes.bytespervox[tp]) *
np.prod(hdr_str_to_np['dims'])
KeyError: 10
resuming program execution
ERROR: some problems occured for the following inputs (see corresponding
errors above):
[mypath]/mri/native.mgz
Error in SynthSeg
Best,
Agata
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