Hi Rito, which freesurfer version are you using here? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ritobrato Datta ribrainsurf@gmail.com Date: Wednesday, August 11, 2021 at 3:01 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] error running samseg on cluster
External Email - Use Caution Hi All,
I am trying to run samseg as follows on a cluster and am getting a message that I need to install tensorflow (which is already installed). Please see below. Please advise how to fix this.
Many thanks
Rito ------------------------------------------------------------- run_samseg --input t12t2.nii.gz t2_brain.nii.gz --lesion --lesion-mask-pattern 0 1 --save-posteriors --output t2_lesions error: This tool requires tensorflow, but fspython does not ship with tensorflow by default. You (or a sys admin) can install the CPU version via:fspython -m pip install tensorflow==1.13.1
fspython -m pip install tensorflow==1.13.1
Requirement already satisfied: tensorflow==1.13.1 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (1.13.1) Requirement already satisfied: protobuf>=3.6.1 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (3.17.3) Requirement already satisfied: keras-applications>=1.0.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.0.8) Requirement already satisfied: absl-py>=0.1.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.13.0) Requirement already satisfied: six>=1.10.0 in /home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) (1.14.0) Requirement already satisfied: grpcio>=1.8.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.39.0) Requirement already satisfied: termcolor>=1.1.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.0) Requirement already satisfied: astor>=0.6.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.8.1) Requirement already satisfied: gast>=0.2.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.5.2) Requirement already satisfied: numpy>=1.13.3 in /home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) (1.18.4) Requirement already satisfied: keras-preprocessing>=1.0.5 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.2) Requirement already satisfied: wheel>=0.26 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.37.0) Requirement already satisfied: tensorboard<1.14.0,>=1.13.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.1) Requirement already satisfied: tensorflow-estimator<1.14.0rc0,>=1.13.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.0) Requirement already satisfied: h5py in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from keras-applications>=1.0.6->tensorflow==1.13.1) (3.1.0) Requirement already satisfied: markdown>=2.6.8 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.3.4) Requirement already satisfied: werkzeug>=0.11.15 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (2.0.1) Requirement already satisfied: mock>=2.0.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow==1.13.1) (4.0.3) Requirement already satisfied: cached-property; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from h5py->keras-applications>=1.0.6->tensorflow==1.13.1) (1.5.2) Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (4.6.3) Requirement already satisfied: dataclasses; python_version < "3.7" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from werkzeug>=0.11.15->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (0.8) Requirement already satisfied: zipp>=0.5 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.5.0) Requirement already satisfied: typing-extensions>=3.6.4; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.10.0.0) You are using pip version 18.1, however version 21.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.