NeuroDock Issues #280
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I am having trouble Running NeuroDock on my computer witch is a Windows 10 64-bit Thinkpad. I was able to download the Docker application, but keep running into a problem when I try to download NeuroDock. This is the error message I get: |
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Replies: 3 comments 35 replies
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Yeah, the container is specified incorrectly. You need to parse in |
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The other issue you'll come across is the way your directory is named. There's a period in your directory, which will break pathing. You need to replace |
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By Parsing do you mean that it needs to broken into two separate commands? |
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It keeps saying the path I am using is not a windows path. |
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Try mounting with a full path that includes the drive i.e. |
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It is very close to running but keeps running into an issue. It keeps saying that it find the neurodock image but I have the Docker Desktop running. |
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So the mounted file is in windows but everything after that is relative to the /data container. I ran the command just like you gave it to me and it still did not work. Not sure why this keeps happening. |
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This is definitely weird. I tried replicating the issue using the same container version on a DICOM directory (Windows as well) and it works just fine on my end. The output should look like the image attached.
One more thing we can try is running MRtrix's |
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Im sorry for all the trouble. I am unsure why my computer is not working correctly. Here is the output when i used the command above. C:\Users\Tash\OneDrive\Documents> |
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That specific |
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Nevermind, I found the issue. There's an extra underscore in your path - it needs to be |
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I think that fixed it the command ran. I am just pasting the output to make sure that it ran everything that it needed to. Does this output show that everything ran correctly?
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No that's not normal. It should have gone to completion at 100%, followed by DTI, DKI and WMTI parameter extraction. I assumed you pasted a part of the output. This happens when you run out of memory. AKC correction is highly demanding in terms of memory. This specific sequence occupies ~20 GB of RAM for AKC correction so I'd suggest allocating at least 16 GB of memory to your Docker containers. Processing can be further sped up by allocating more CPU cores to your containers. Docker's documentation covers how to do both of these on Windows systems. I primarily use FSLeyes for visualization of output NifTi files. A VM running Ubuntu or headless Ubuntu installation on WSL will allow you to get it to work on Windows. Otherwise, tools like ImageJ Fiji or Mango also work. |
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Sorry for taking so long to respond. We recently received a hard drive that I am trying to use for the processing to help with the space issue. Do I have to place the docker in the hard drive folder? Also, I have been trying to set up the path to mount the file in the hard drive but I keep receiving an error message. Is this the correct way to mount it on to the hard drive? The letter given to the hard drive is D |
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I was able to run the command using the hard drive as the mounted file but it did not go through the whole processing. I pasted the output below. Im not sure what went wrong. C:\Users\Tash>docker run -it --rm -v D:\DKE:/data dmri/neurodock:latest pydesigner --standard --output /data/output /data/DKI_BIPOLAR_2_5mm_64dir_50slices_20 C:\Users\Tash> |
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Hi @mmsarhan, you do not need to reinstall NeuroDock again since it resides on your host OS drive just like any other software. I've never seen that error before but it appears that a certain preprocessing file was not created. Could you delete all contents of the output folder and rerun processing with the addition of a |
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I am not sure why, but when I run the command it does not work anymore. Even when I add the --verbose it does not work. I have both outputs with and without --verbose to show it does not work. Im not sure why its not working. C:\Users\Tash>docker run -it --rm -v D:\DKE:/data dmri/neurodock:latest pydesigner --standard --output /data/output /data/DKI_BIPOLAR_2_5mm_64dir_50slices_20 C:\Users\Tash>docker run -it --rm -v D:\DKE:/data dmri/neurodock:latest pydesigner --standard --output --verbose /data/output /data/DKI_BIPOLAR_2_5mm_64dir_50slices_20 C:\Users\Tash> |
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It is very close to running but keeps running into an issue. It keeps saying that it find the neurodock image but I have the Docker Desktop running.