ANTsPyNet installation error: Tensorflow not found

[hegde00]

Hi Everyone,

I'm trying to install ANTsPyNet using the instructions in https://github.com/ANTsX/ANTsPyNet.

Everything seemed to go well (please see the attached log), except that the final command generates a "tensorflow distribution not found" error as follows:

jay@Euler:/ANTsPyNet$ sudo python3 setup.py install
...
...
Installed /usr/local/lib/python3.8/dist-packages/tfp_nightly-0.2.0.dev20220302-py3.8.egg
error: The 'tensorflow' distribution was not found and is required by antspynet
jay@Euler:/ANTsPyNet$

Can you please help? Thank you!
Jay

ANTsPyNet_installation_log_JayHegde.txt

[ntustison]

What happens when you actually try to import ANTsPy and ANTsPyNet?

>>> import ants
>>> import antspynet

[hegde00]

HI Nick,

I ran your suggested commands from my Python3 prompt (I assumed this is what you meant, judging from the prompt sign). Here's what I got:

import ants #Seems to have worked fine.
import antspynet
2022-03-03 07:57:29.305885: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2022-03-03 07:57:29.305925: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.

Thanks,
Jay

[ntustison]

Okay, those errors are probably fine. If you do have a GPU available for processing, you'll have to set it up separately. For now, try a t1-w brain extraction---

>>> import ants
>>> import antspynet
>>> t1 = ants.image_read(antspynet.get_antsxnet_data("kirby"))
>>> mask = antspynet.brain_extraction(t1, modality="t1", verbose=True)

[hegde00]

I think it worked! Please see below. Thank you very much, Nick! So may I assume that ANTsPyNet is set up correctly on my machine and proceed accordingly? (I'll look into setting up my GPU (I do have an NVIDIA graphics card on this machine).

Jay

import ants
import antspynet
t1 = ants.image_read(antspynet.get_antsxnet_data("kirby"))
Downloading data from https://ndownloader.figshare.com/files/25620107
39452672/39448573 [==============================] - 78s 2us/step
39460864/39448573 [==============================] - 78s 2us/step
mask = antspynet.brain_extraction(t1, modality="t1", verbose=True)
Brain extraction: retrieving model weights.
...
Brain extraction: normalizing image to the template.
Brain extraction: prediction and decoding.
1/1 [==============================] - 2s 2s/step
Brain extraction: renormalize probability mask to native space.
mask
ANTsImage (LAI)
Pixel Type : float (float32)
Components : 1
Dimensions : (170, 256, 256)
Spacing : (1.2, 1.0, 1.0)
Origin : (202.8, 0.0, 0.0)
Direction : [-1. 0. 0. 0. 1. 0. 0. 0. 1.]

[ntustison]

So may I assume that ANTsPyNet is set up correctly on my machine and proceed accordingly?

It appears to be.

(I'll look into setting up my GPU (I do have an NVIDIA graphics card on this machine).

Unless you're training models, this is probably not of significant priority. All of the processing I do on the university cluster doesn't utilize the GPUs as CPU-based processing is sufficiently fast and the number of CPU units >> number of GPU units.

[hegde00]

Thank you very much. I greatly appreciate it. Please consider this issue resolved then.