External Email - Use Caution Hi all, I've downloaded a new dev version of FS 7/19/2022 - and I receive an error with running subunits:
mri_segment_hypothalamic_subunits --s 10893/ using 1 thread /mnt/QBERT/freesurfer/python/scripts/mri_segment_hypothalamic_subunits:1023: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj). * deprecated from version: 3.0 * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0 volume = np.squeeze(x.get_data()) predicting 1/1 the following problem occured when preprocessing image /..../0893/mri/nu.mgz : 'NoneType' object is not subscriptable resuming program execution segmentation saved in: /..../10893/mri/hypothalamic_subunits_seg.v1.mgz volumes saved in: /..../10893/mri/hypothalamic_subunits_volumes.v1.csv resampled images saved in: /..../10893/mri/hypothalamic_subunits_nu_resampled_1mm.v1.mgz If you use this tool in a publication, please cite: Automated segmentation of the hypothalamus and associated subunits in brain MRI B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, J. E. Iglesias NeuroImage 2020 Is this a problem with tensorflow? It does not seem clear. No files are actually being written Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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