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MASILab / Synb0-DISCO

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps
https://my.vanderbilt.edu/masi
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Problems installing Synb0 with undockerized and dockerized singularity instructions #41

Closed alestella closed 1 year ago

alestella commented 1 year ago

Good morning, I am trying to use Synb0-DISCO in a Ubuntu 20.04 operating system. I have two distinct problems, one with the undockerized and one with the dockerized singularity modality.

(UNSOLVED) AS per the undockerized instructions, I have successfully run the program (after modifying the paths so that the pipeline.sh pointed at the FSL, Freesurfer, ANTs and Pytorch). However, when running c3d_affine_tool, the function keeps looking for the library libITKIOGDCM-5.2.so.1, whereas in the /usr/local/fsl/...fslpython/lib folder there is only libITKIOGDCM-5.1.so.1! I cannot find the other library, even If I wanted to download it separately.

(SOLVED) As per the dockerized singularity modality, I am having problem because, although my /tmp folder has a capacity of over 200 GB, towards the end of the pulling (singularity pull docker://leonyichencai/synb0-disco:v3.0), it says 'FATAL: ...no space left on device'. Do you have any idea on how to go on from here?

Any help is very much appreciated, thank you!

alestella commented 1 year ago

image

schillkg commented 1 year ago

That is very strange that it is taking up so much space on download. Could you try downloading the container to any other machine then copying? I believe the container is only ~12Gb. Are you somehow pulling the image for each time you call the container?

alestella commented 1 year ago

(SOLVED) Good morning! I have deleted the previous docker images, and started from fresh. However, I still get a 'no space left on device' error: image

UPDATE: I solved this issue by cleaning the docker images I was not using (docker system prune -a), then I managed to pull the docker and run the program successfully!