On Feb 25, 2024, at 21:45, Agata Wolna <awolna@mit.edu> wrote:

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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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