Dear Niels,
Would it be possible to share T1w_acpc_dc_restore_1mm.nii.gz with us so we can try on our end?
Cheers,
Eugenio
Juan Eugenio Iglesias http://www.jeiglesias.com
On 9 Mar 2022, at 09:16, Niels Janssen <njanssen@ull.edu.esmailto:njanssen@ull.edu.es> wrote:
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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://sites.google.com/view/nielsjanssen/https://secure-web.cisco.com/1k8Xn2D4J0byFyRwIbmBKVyMDjJThmhtuWNmuBVgygLkSVhxxPebqS7fYo4B7MWMirKuq5EEUt1IbYcelrWvGTKP0ZSVQ13IzPa6F-bBFGyDEVco097MGKGNKimELqErooVe13creAe1LKe_UOvX3wUVBkQ4wW7ehVp5SyN9tNsrJx4hmqUrlCRdvBGMaTpXov2G4O0n_6wIHKxDc1DGbEjq6X4kwYm8jVenxYxX29kYRjlAtOqrWGTfei3bbznPzC3Gb7y4onNieR0gmEMKSe9iBy5f5AQAw2DtWTFwU-_pEAcUaHXGgRxd-9Z4L7Cv1/https%3A%2F%2Fsites.google.com%2Fview%2Fnielsjanssen%2F _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer