Hi Jonathan,
I believe running this should do the trick:
fspython -m pip install h5py==2.10.0
Best,
Andrew
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jonathan A Winawer <jonathan.winawer@nyu.edu>
Date: Wednesday, August 18, 2021 at 12:03 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] infant freesurfer
External Email - Use Caution
Dear All,
I am running into errors using the infant freesurfer tool. Specifically, the error I am getting now is this:
Traceback (most recent call last):
File "/Applications/freesurfer/infantFreesurfer/python/scripts/sscnn_skullstrip", line 74, in <module>
cor_img_data = predict('cor')
File "/Applications/freesurfer/infantFreesurfer/python/scripts/sscnn_skullstrip", line 64, in predict
wmp_standardize=False
File "/Applications/freesurfer/infantFreesurfer/python/packages/sscnn_skullstripping/deeplearn_utils/DeepImageSynth.py", line 261, in from_file
model = load_model(model_filename, custom_objects={'dice_coef_loss2': dice_coef_loss2})
File "/Applications/freesurfer/infantFreesurfer/python/lib/python3.6/site-packages/keras/engine/saving.py", line 259, in load_model
model_config = json.loads(model_config.decode('utf-8'))
AttributeError: 'str' object has no attribute 'decode'
Maybe the skull stripping is failing because of the shoulders in the image?
--
Jonathan Winawer
Associate Professor of Psychology and Neural Science
New York University
6 Washington Place
New York, NY, 10003
(212) 998-7922 (phone)
(212) 995-4018 (fax)