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I am trying to run the hypothalamic subunits segmentation but I am getting
an error message (see below).
I have FS7.2 installed on Ubuntu 18.04 (hippocampal and thalamic nuclei
work fine).
This error occurs even after changing the voxel size to 1x1x1 as per the
instructions (because this is HCP data with 0.7mm).
Thanks for your help
Niels
---------------
nielsj@vein:/ImageData/DataSets/HCP/3T/100206/T1w$
mri_segment_hypothalamic_subunits --i T1w_acpc_dc_restore_1mm.nii.gz --o
test
using 1 thread
processing 1/1
Traceback (most recent call last):
File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 1463, in <module>
main()
File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 90, in main
threads=args.threads
File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 164, in predict
net = build_model(path_model, model_input_shape, len(label_list))
File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 577, in build_model
input_model=None)
File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 750, in unet
input_model=enc_model)
File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 948, in conv_dec
last_tensor = keras.layers.concatenate([cat_tensor, last_tensor],
axis=ndims + 1, name=name)
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py",
line 931, in concatenate
return Concatenate(axis=axis, **kwargs)(inputs)
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 952, in __call__
input_list)
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 1091, in _functional_construction_call
inputs, input_masks, args, kwargs)
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 822, in _keras_tensor_symbolic_call
return self._infer_output_signature(inputs, args, kwargs, input_masks)
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 862, in _infer_output_signature
self._maybe_build(inputs)
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 2710, in _maybe_build
self.build(input_shapes) # pylint:disable=not-callable
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/utils/tf_utils.py",
line 272, in wrapper
output_shape = fn(instance, input_shape)
File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py",
line 519, in build
raise ValueError(err_msg)
ValueError: A `Concatenate` layer requires inputs with matching shapes
except for the concat axis. Got inputs shapes: [(None, 176, 184, 176, 24),
(None, 48, 184, 176, 480)]
--
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Institute of Neurosciences
University of La Laguna
Tenerife, Spain
https://secure-web.cisco.com/1k8Xn2D4J0byFyRwIbmBKVyMDjJThmhtuWNmuBVgygLkSVhxxPebqS7fYo4B7MWMirKuq5EEUt1IbYcelrWvGTKP0ZSVQ13IzPa6F-bBFGyDEVco097MGKGNKimELqErooVe13creAe1LKe_UOvX3wUVBkQ4wW7ehVp5SyN9tNsrJx4hmqUrlCRdvBGMaTpXov2G4O0n_6wIHKxDc1DGbEjq6X4kwYm8jVenxYxX29kYRjlAtOqrWGTfei3bbznPzC3Gb7y4onNieR0gmEMKSe9iBy5f5AQAw2DtWTFwU-_pEAcUaHXGgRxd-9Z4L7Cv1/https%3A%2F%2Fsites.google.com%2Fview%2Fnielsjanssen%2F
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