External Email - Use Caution It could help to know what OS version and what Freesurfer version you are running. From your path /usr/local/freesurfer it looks like you are running a Freesurfer release, e.g., 7.4.1. - R.
On Feb 25, 2024, at 21:45, Agata Wolna <awo...@mit.edu> wrote: External Email - Use Caution 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: 10resuming program executionERROR: some problems occured for the following inputs (see corresponding errors above):[mypath]/mri/native.mgzError in SynthSegBest,Agata_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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