Hi Alex,

After sourcing the dev distribution, can you run:

fspython -m pip install h5py==2.10.0

This is an unfortunate bug with older versions of keras and newer versions of h5py, but we’ll be upgrading our internal scripts soon to deal with this. Thanks for point this out - I’ll put a note in the dev TF-install instructions.

As for dealing with multiple FS versions, just install them in different directories. Something like:

/path/to/freesurfer/6.0.0 /path/to/freesurfer/7.1.1 /path/to/freesurfer/dev etc…

Best, Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience ladn@email.gwu.edu Date: Tuesday, February 2, 2021 at 1:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

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 <dgreve@mgh.harvard.edumailto:dgreve@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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