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Thank you for your comment.
I did as you suggested: I first uninstalled freesurfer 7.4.1 and then installed the beta 8.0.0. The installation was successful, but the problem remained, with the same error message.
Does any other solution come to your mind?
Thank you again, Giuseppe
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of fsbuild Sent: 08 February 2025 02:39 To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNE-EMAIL] Re: [Freesurfer] mri_synthSR on a virtual machine. Graph execution error
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I would try using the recent freesurfer 8.0.0 beta release package installer which you can download from,
https://secure-web.cisco.com/1BaaVMIMg4MlAs7yuAfUHy21mKi-yLQu7A8gJLdmc-PtHqA... The links for those are at the top of the page.
I would first uninstall the current freesurfer package, e.g. $ sudo apt remove freesurfer
.... and then install the .deb package for the 8.0.0 beta release
- R.
On 2/7/25 03:27, Zito Giuseppe (giuseppe.zito@paraplegie.chmailto:giuseppe.zito@paraplegie.ch) wrote:
External Email - Use Caution 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 FS7_wsl_ubuntu - Free Surfer Wikihttps://secure-web.cisco.com/12twtudy3gB_NJlsrHFZDE-M9SwSDMGFINdPbZcIDLWt1EwzLDqsUhSfAaf9AAmSJMXVHlTYFBJcnC3BRby6YYrPvoyNBxjwYu8wE5I3jDuyx8wcNh7YItx7TFGLPh0lkcEFhGA3FdWpFmhjsEMQyvlDxeNs5mjjgQNAcbfOKgNzHeZSp2htBvtqgP6wuW7gvpelFy0_y7Zx5pmPQ3NB8RsVAyXcNxe3n_6O4zXRFnbwLvARbIjq9T02qQ7pKcGCDogJJ3ViR_gV6bRt7orbZg292JZ99qQWq509tAa3ymKuCTDO3Ipyt1kdrO9Q-mtzVMsVXYV0_UWfBoaCGfrGPaw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
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
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