On 9 Mar 2022, at 09:16, Niels Janssen <njanssen@ull.edu.es> wrote:

        External Email - Use Caution        

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/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer