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Hi Freesurfer,
Does anyone know what to do with this error when running run_samseg --input T1.filename FLAIR.filename --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /samsegOutput/

OSError: [Errno 30] Read-only file system: '/samsegOutput/'

Many thanks.
AJ

On Sun, Apr 18, 2021, 21:31 AJ <ajcns1969@gmail.com> wrote:
I greatly appreciate your help, Vishnu.

This is the error I get now.:

(base) MacBook-Pro-4:aseg2620145_2018 AJ$ conda activate myenv

(myenv) MacBook-Pro-4:aseg2620145_2018 AJ$ fspython -m pip install tensorflow==1.13.1 --user admin

Requirement already satisfied: tensorflow==1.13.1 in /Users/AJ/.local/lib/python3.6/site-packages (1.13.1)

Requirement already satisfied: admin in /Users/AJ/.local/lib/python3.6/site-packages (0.0.1)

Requirement already satisfied: absl-py>=0.1.6 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.12.0)

Requirement already satisfied: six>=1.10.0 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1) (1.14.0)

Requirement already satisfied: termcolor>=1.1.0 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.0)

Requirement already satisfied: wheel>=0.26 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.36.2)

Requirement already satisfied: gast>=0.2.0 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.4.0)

Requirement already satisfied: numpy>=1.13.3 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1) (1.18.4)

Requirement already satisfied: tensorflow-estimator<1.14.0rc0,>=1.13.0 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.0)

Requirement already satisfied: protobuf>=3.6.1 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (3.15.8)

Requirement already satisfied: grpcio>=1.8.6 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.37.0)

Requirement already satisfied: keras-applications>=1.0.6 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.0.8)

Requirement already satisfied: astor>=0.6.0 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.8.1)

Requirement already satisfied: keras-preprocessing>=1.0.5 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.2)

Requirement already satisfied: tensorboard<1.14.0,>=1.13.0 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.1)

Requirement already satisfied: mock>=2.0.0 in /Users/AJ/.local/lib/python3.6/site-packages (from tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow==1.13.1) (4.0.3)

Requirement already satisfied: h5py in /Users/AJ/.local/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 /Users/AJ/.local/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 /Users/AJ/.local/lib/python3.6/site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (1.0.1)

Requirement already satisfied: cached-property; python_version < "3.8" in /Users/AJ/.local/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 /Users/AJ/.local/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (4.0.0)

Requirement already satisfied: typing-extensions>=3.6.4; python_version < "3.8" in /Users/AJ/.local/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) (3.7.4.3)

Requirement already satisfied: zipp>=0.5 in /Users/AJ/.local/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) (3.4.1)

You are using pip version 18.1, however version 21.0.1 is available.

You should consider upgrading via the 'pip install --upgrade pip' command.

(myenv) MacBook-Pro-4:aseg2620145_2018 AJ$ run_samseg --input 3DT1_output.nii FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /samsegOutput/

/Users/AJ/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.

  _np_qint8 = np.dtype([("qint8", np.int8, 1)])

/Users/AJ/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:527: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.

  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])

/Users/AJ/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:528: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.

  _np_qint16 = np.dtype([("qint16", np.int16, 1)])

/Users/AJ/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:529: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.

  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])

/Users/AJ/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:530: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.

  _np_qint32 = np.dtype([("qint32", np.int32, 1)])

/Users/AJ/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:535: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.

  np_resource = np.dtype([("resource", np.ubyte, 1)])

Traceback (most recent call last):

  File "/Applications/freesurfer/7.1.0//python/scripts/run_samseg", line 61, in <module>

    os.makedirs(args.outputDirectory, exist_ok=True)

  File "/Applications/freesurfer/7.1.0//python/lib/python3.6/os.py", line 220, in makedirs

    mkdir(name, mode)

OSError: [Errno 30] Read-only file system: '/samsegOutput/'

(myenv) MacBook-Pro-4:aseg2620145_2018 AJ$ 


On Sun, Apr 18, 2021 at 9:26 PM Vishnu S <vishnudaboss@gmail.com> wrote:

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No instead of --admin permissions it would be --user

On Mon, 19 Apr 2021, 07:24 AJ, <ajcns1969@gmail.com> wrote:

        External Email - Use Caution        

Thank you for your response.

Would that script be fspython -m pip install tensorflow==1.13.1 --admin permissions

On Sat, Apr 17, 2021, 20:33 Vishnu S <vishnudaboss@gmail.com> wrote:

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Can you try running the same command with the --user flag (admin permissions)?

On Sun, 18 Apr 2021, 00:40 AJ, <ajcns1969@gmail.com> wrote:

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Thank you for your help.  I think I'm getting closer to installing tensor flow.
1-as you suggested:  installed .NET

(myenv) MacBook-Pro-4:~ AJ$ dotnet --info
.NET SDK (reflecting any global.json):
 Version:   5.0.202
 Commit:    db7cc87d51

Runtime Environment:
 OS Name:     Mac OS X
 OS Version:  10.15
 OS Platform: Darwin
 RID:         osx.10.15-x64
 Base Path:   /usr/local/share/dotnet/sdk/5.0.202/

Host (useful for support):
  Version: 5.0.5
  Commit:  2f740adc14

.NET SDKs installed:
  5.0.202 [/usr/local/share/dotnet/sdk]

.NET runtimes installed:
  Microsoft.AspNetCore.App 5.0.5 [/usr/local/share/dotnet/shared/Microsoft.AspNetCore.App]
  Microsoft.NETCore.App 5.0.5 [/usr/local/share/dotnet/shared/Microsoft.NETCore.App]

To install additional .NET runtimes or SDKs:
  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://aka.ms/dotnet-download

(myenv) MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.13.1
Collecting tensorflow==1.13.1
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Collecting keras-preprocessing>=1.0.5 (from tensorflow==1.13.1)
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Collecting astor>=0.6.0 (from tensorflow==1.13.1)
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Collecting wheel>=0.26 (from tensorflow==1.13.1)
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Collecting absl-py>=0.1.6 (from tensorflow==1.13.1)
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Collecting tensorboard<1.14.0,>=1.13.0 (from tensorflow==1.13.1)
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Collecting gast>=0.2.0 (from tensorflow==1.13.1)
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Collecting keras-applications>=1.0.6 (from tensorflow==1.13.1)
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Collecting tensorflow-estimator<1.14.0rc0,>=1.13.0 (from tensorflow==1.13.1)
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Collecting termcolor>=1.1.0 (from tensorflow==1.13.1)
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Collecting grpcio>=1.8.6 (from tensorflow==1.13.1)
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Requirement already satisfied: six>=1.10.0 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1) (1.14.0)
Requirement already satisfied: numpy>=1.13.3 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1) (1.18.4)
Collecting protobuf>=3.6.1 (from tensorflow==1.13.1)
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Collecting werkzeug>=0.11.15 (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1)
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Collecting markdown>=2.6.8 (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1)
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Collecting h5py (from keras-applications>=1.0.6->tensorflow==1.13.1)
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Collecting mock>=2.0.0 (from tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow==1.13.1)
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Collecting importlib-metadata; python_version < "3.8" (from markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1)
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Collecting cached-property; python_version < "3.8" (from h5py->keras-applications>=1.0.6->tensorflow==1.13.1)
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Collecting zipp>=0.5 (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1)
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Collecting typing-extensions>=3.6.4; python_version < "3.8" (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1)
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Installing collected packages: keras-preprocessing, astor, wheel, absl-py, werkzeug, protobuf, grpcio, zipp, typing-extensions, importlib-metadata, markdown, tensorboard, gast, cached-property, h5py, keras-applications, mock, tensorflow-estimator, termcolor, tensorflow
Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/Applications/freesurfer/7.1.0/python/lib/python3.6/site-packages/keras_preprocessing'
Consider using the `--user` option or check the permissions.

Not sure what the EnvironmentError is?  The myenv was set up as:
conda create -n myenv python=3.6
conda activate myenv

Many thanks.

AJ

On Fri, Apr 16, 2021 at 11:38 PM Vishnu S <vishnudaboss@gmail.com> wrote:

        External Email - Use Caution        


On Sat, 17 Apr 2021, 09:33 AJ, <ajcns1969@gmail.com> wrote:

        External Email - Use Caution        

sorry, but I get the same error after
conda create -n myenv python=3.6
conda activate myenv

(myenv) MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.13.1
Collecting tensorflow==1.13.1
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Requirement already satisfied: numpy>=1.13.3 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1) (1.18.4)
Collecting keras-preprocessing>=1.0.5 (from tensorflow==1.13.1)
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Collecting keras-applications>=1.0.6 (from tensorflow==1.13.1)
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Collecting tensorboard<1.14.0,>=1.13.0 (from tensorflow==1.13.1)
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Collecting tensorflow-estimator<1.14.0rc0,>=1.13.0 (from tensorflow==1.13.1)
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Collecting gast>=0.2.0 (from tensorflow==1.13.1)
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Collecting absl-py>=0.1.6 (from tensorflow==1.13.1)
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Requirement already satisfied: six>=1.10.0 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1) (1.14.0)
Collecting grpcio>=1.8.6 (from tensorflow==1.13.1)
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Collecting wheel>=0.26 (from tensorflow==1.13.1)
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Collecting protobuf>=3.6.1 (from tensorflow==1.13.1)
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Collecting termcolor>=1.1.0 (from tensorflow==1.13.1)
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dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

Abort trap: 6

On Fri, Apr 16, 2021 at 10:36 PM AJ <ajcns1969@gmail.com> wrote:
thank you so much.  I just installed conda.
(base) MacBook-Pro-4:~ AJ$ conda -V
conda 4.9.2
Is myenv /Aplications/freesurfer/7.1.0
thank you.
aj

On Fri, Apr 16, 2021 at 10:22 PM Vishnu S <vishnudaboss@gmail.com> wrote:

        External Email - Use Caution        

1. Make sure you have conda installed 
2. In your terminal, then

conda create -n myenv python=3.6
conda activate myenv

3. Then you should be able to install TF 1.13

On Sat, 17 Apr 2021, 08:46 AJ, <ajcns1969@gmail.com> wrote:

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sorry for being non-tech, but how do I exactly do creating a conda venv with Python 3.6.
many thanks
aj

On Fri, Apr 16, 2021 at 9:56 PM Vishnu S <vishnudaboss@gmail.com> wrote:

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Hi AJ,

So tensorflow 1.13.0 is looking for Python 3.6 as far as I know. Python >=3.7 only supports TF2. Can you try creating a conda venv with Python 3.6 and try again?

On Sat, 17 Apr 2021, 08:23 AJ, <ajcns1969@gmail.com> wrote:

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Thank you so much for your help.
Here's the error:
MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.15
Collecting tensorflow==1.15
  Using cached MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://files.pythonhosted.org/packages/fe/01/997a5d608162cf5371dae49e8cb68baaa5773b091a3e74576ea30dae51e6/tensorflow-1.15.0-cp36-cp36m-macosx_10_11_x86_64.whl
Requirement already satisfied: six>=1.10.0 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15) (1.14.0)
Collecting keras-applications>=1.0.8 (from tensorflow==1.15)
  Using cached MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl
Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15)
  Downloading MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://files.pythonhosted.org/packages/de/62/2ee9cd74c9fa2fa450877847ba560b260f5d0fb70ee0595203082dafcc9d/tensorflow_estimator-1.15.1-py2.py3-none-any.whl (503kB)
    100% |████████████████████████████████| 512kB 5.8MB/s
Collecting opt-einsum>=2.3.2 (from tensorflow==1.15)
  Downloading MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://files.pythonhosted.org/packages/bc/19/404708a7e54ad2798907210462fd950c3442ea51acc8790f3da48d2bee8b/opt_einsum-3.3.0-py3-none-any.whl (65kB)
    100% |████████████████████████████████| 71kB 13.9MB/s
Requirement already satisfied: numpy<2.0,>=1.16.0 in /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15) (1.18.4)
Collecting absl-py>=0.7.0 (from tensorflow==1.15)
  Using cached MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://files.pythonhosted.org/packages/92/c9/ef0fae29182d7a867d203f0eff8296b60da92098cc41db33a434f4be84bf/absl_py-0.12.0-py3-none-any.whl
Collecting wrapt>=1.11.1 (from tensorflow==1.15)
  Using cached MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://files.pythonhosted.org/packages/82/f7/e43cefbe88c5fd371f4cf0cf5eb3feccd07515af9fd6cf7dbf1d1793a797/wrapt-1.12.1.tar.gz
dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

Abort trap: 6



On Fri, Apr 16, 2021 at 12:45 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Hi AJ,

 

Freesurfer ships its own python distribution, so it doesn’t matter what you have installed on your system. Can you let us know the specific version of macOS you are using and send the full error report from pip?

 

Thanks

Andrew

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AJ <ajcns1969@gmail.com>
Date: Friday, April 16, 2021 at 11:56 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] error installing tensorflow

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Hi,

I have python both versions of python installed:

MacBook-Pro-4:~ AJ$ python3 --version
Python 3.9.4
MacBook-Pro-4:~ AJ$ python --version
Python 2.7.10

 

when installing  fspython -m pip install tensorflow==1.13.1, I get the error:

dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

Abort trap: 6

 

Is the issue that freesurfer is looking for python3?  I am not sure how to get past this installation of tensorflow?

Thank you for your help.

AJ

 

 

On Fri, Apr 16, 2021 at 12:58 AM Vishnu S <vishnudaboss@gmail.com> wrote:

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Can you try downgrading to python 3.6 in a conda env? Python 3.7 support only TF 2.0 and higher. 

 

On Fri, 16 Apr 2021, 11:24 AJ, <ajcns1969@gmail.com> wrote:

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Hi,

 

I am having trouble installing:  fspython -m pip install tensorflow==1.13.1

Not sure what the issue is.  Any help would be greatly appreciated.

best

AJ

Error message while installing:


dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3

  Expected in: /usr/lib/libSystem.B.dylib

 

 

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