Dear experts,
I just installed freesurfer on a windows virtual machine. It is a windows virtual machine, in the sense that I have a windows machine, on which is installed a virtual windows machine, in which is installed Ubuntu with WSL2 (nested virtual machine).
I have then installed FreeSurfer by following the instructions on this page
When I tried to use mri_synthsr to convert a Flair image into a T1, I get the following error. No T1 file is then generated.
Does anyone have an idea of what could go have gone wrong?
Thank you very much,
Giuseppe
My command line
mri_synthsr --i 3D_FLAIR.nii --o 3D_T1converted.nii
Output from the software
Using general model from January 2023 (version 2)
/usr/local/freesurfer/7.4.1/models/synthsr_v20_230130.h5
using 1 thread
predicting 1/1
Prediction without flipping
the following problem occured when predicting output for image /mnt/c/AIR_Software/SynthSR/3D_FLAIR.nii :
Graph execution error:
Detected at node 'unet/unet_merge_8/concat' defined at (most recent call last):
File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 1227, in <module>
main()
File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 88, in main
predict(
File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 151, in predict
pred1 = np.squeeze(net.predict(image))
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2382, in predict
tmp_batch_outputs = self.predict_function(iterator)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2169, in predict_function
return step_function(self, iterator)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2155, in step_function
outputs = model.distribute_strategy.run(run_step, args=(data,))
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2143, in run_step
outputs = model.predict_step(data)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2111, in predict_step
return self(x, training=False)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 558, in __call__
return super().__call__(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__
outputs = call_fn(inputs, *args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler
return fn(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/functional.py", line 512, in call
return self._run_internal_graph(inputs, training=training, mask=mask)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/functional.py", line 669, in _run_internal_graph
outputs = node.layer(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__
outputs = call_fn(inputs, *args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler
return fn(*args, **kwargs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/layers/merging/base_merge.py", line 196, in call
return self._merge_function(inputs)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/layers/merging/concatenate.py", line 134, in _merge_function
return backend.concatenate(inputs, axis=self.axis)
File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/backend.py", line 3581, in concatenate
return tf.concat([to_dense(x) for x in tensors], axis)
Node: 'unet/unet_merge_8/concat'
OOM when allocating tensor with shape[1,192,256,256,72] and type float on /job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu
[[{{node unet/unet_merge_8/concat}}]]
Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info. This isn't available when running in Eager mode.
[Op:__inference_predict_function_2117]
resuming program execution