External Email - Use Caution
Thank you for your help!
I have tested the hypothalamus segmentation on the development version of
FS, and this was the error output that I got (see below). How should I
proceed to fix this?
:~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003_srs2
Using 1 thread
2021-02-02 12:19:04.878273: I
tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-02-02 12:19:04.899000: I
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:
2999995000 Hz
2021-02-02 12:19:04.899178: I
tensorflow/compiler/xla/service/service.cc:150] XLA service 0x20b88f0
executing computations on platform Host. Devices:
2021-02-02 12:19:04.899215: I
tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device
(0): <undefined>, <undefined>
processing 1/1
Traceback (most recent call last):
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 1464, in <module>
main()
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 91, in main
threads=args.threads
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 165, in predict
net = build_model(path_model, model_input_shape, len(label_list))
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 579, in build_model
net.load_weights(model_file, by_name=True)
File
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py",
line 1514, in load_weights
saving.load_weights_from_hdf5_group_by_name(f, self.layers)
File
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/saving.py",
line 839, in load_weights_from_hdf5_group_by_name
original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'
Also, what's the best way for me to run a second version of Freesurfer on
the same computer? I used a virtualbox, but is there a way to run it
outside of that?
Thank you so much for the help and stay safe,
Alex
On Sat, Jan 30, 2021 at 1:25 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:
> It is not in version 7. You'll have to download a development version of
> FS to run it.
>
> On 1/29/2021 9:26 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I am having some trouble getting the hypothalamus segmentation recognized
> on the command line for FreeSurfer 7.1.0. Is it even available for this
> version? If not, will it work on the 6.0 or the 7.1.1 version?
>
> Thanks and stay safe!
>
> All the best,
> Alex
>
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