-
Notifications
You must be signed in to change notification settings - Fork 73
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
No such file or no access: 'tractseg_output/peaks.nii.gz' #1
Comments
The docker container provided in the repository is still work in progress (WIP). It does not work yet, because the FSL and Mrtrix commands are not automatically loaded (.bashrc is not automatically sourced). Apart from that the docker container is ready. I will try to fix this issue soon. |
I just realized you are using the docker container from gkoehler90/tractseg. That one is out-dated. As soon as I fixed the docker issue mentioned in the previous comment I will push a new docker image to dockerhub. Until then you should use TractSeg without Docker (or build your own docker container). |
@wasserth Thank you for looking into the container issue. I did try to run it without it by installing various dependencies, but I couldn't get it to work after messing around for a while. I can wait for the container to be updated. |
@soichih I fixed the issues and now it should work using the following command:
On OSX you might have to increase the Docker Memory limit from the default of 2GB to something higher. |
Great! Thanks! I just tested it again (I have to use singularity for our HPC system)
Maybe FSL is not in the PATH? |
When I run the docker container FSL is in the PATH. So it is strange that it does not find it when you run it with singularity. |
I've cleaned the ~/.singularity/docker directory and rerun, but I am still seeing the same error message.
I've also tried running singularity witih -e option which prevents ENV parameter on the host to be set inside the container, but that didn't help either. I think the issue is related to singularity but I haven't really looked into it yet. |
Sorry for the late reply. I was on vacation last week. |
OK. I've created my own Dockerfile that works for our environment. Tractseg now seems to work via singularity! The first thing I noticed though, is that it's downloading the trained model under $HOME/.tractseg. Is there anyway I could pre-stage the model and make it part of my Docker container? - maybe by doing something like nvm.. I found this on the official Dockerfile
|
Great that it works. So far there is not option to change the tractseg home directory from |
I am running it through singularity, and it mounts host's home directory by default - wiping out the container's home directory (/root for docker?). I've done following to hack around it.
It's ugly.. but it seems to work for now. It would be nice to be able to specify the directory where model is stored though! :) |
Hello!
I am trying to run TractSeg via singularity like the following
I have following files in my local directory.
When I run it, I get following error messages.
On my current directory, I see an empty directory created with the name "tracseg_output".
Am I running this in a wrong way?
The text was updated successfully, but these errors were encountered: