TVB-ukbb

[MICHELANGELO FABBRIZZI]

Dear TVB experts,

it looks my MRI data do not include the fieldmap as required to use the EBRAINS TVB Pipeline https://wiki.ebrains.eu/bin/view/Collabs/tvb-pipeline/ .

Hence I am trying to use the TVB-ukbb pipeline available at https://github.com/McIntosh-Lab/tvb-ukbb/ , however I get a erros during installation. I am using a local machine with MacOS Monterey.

I followed the guide at https://github.com/McIntosh-Lab/tvb-ukbb/wiki/Installing-on-a-General-HPC-System :

- I installed Vagrant and Singularity as described at https://docs.sylabs.io/guides/3.2/user-guide/installation.html#mac

- when pulling the Singularity container "singularity pull library://noahfl/tvb/tvb-ukbb:latest" I get an error "FATAL:   While getting image info: error decoding image: invalid ObjectId in JSON: "noahfl/tvb/tvb-ukbb:sha256.840a4427e34241fee7033ecebdcb4215a1256c77280ddf21d8ffdba149006947"

- even trying the pull commands at https://cloud.sylabs.io/library/noahfl/tvb/tvb-ukbb or trying to click Download, it looks it gets stuck.

Similarly if I download the Installer at https://github.com/McIntosh-Lab/tvb-ukbb/releases/tag/1.3 and then run the script file install_ukbb_singularity.sh , I get the following error:

Solving environment: failed

ResolvePackageNotFound: 

  - noahfl::gradunwarp

I see that the Installer files include also the following, can they help me:

- install_ukbb_norepo.sh

- install_ukbb.sh

I am not using them since the Wiki of the TVB-ukbb and the corresponding paper are suggesting to use the Singularity container to simplify the installation and use.

I would be grateful if anyone could help me with the above.

Appreciated, thanks,

Michelangelo

[MICHELANGELO FABBRIZZI]

Dear all,

just an update, after manually downloading the .sif from https://cloud.sylabs.io/library/noahfl/tvb/tvb-ukbb and renaming to tvb-ukbb.sif , launching Vagrant and then executing as stated in the guide at https://github.com/McIntosh-Lab/tvb-ukbb/wiki/Installing-on-a-General-HPC-System the command singularity shell --nv -B /home /vagrant/tvb-ukbb.sif  (in the Virtual Machine created with Vagrant, the .sif file is located in the directory /vagrant), I get an error:

FATAL:   container creation failed: mount /proc/self/fd/5->/usr/local/var/singularity/mnt/session/rootfs error: can't mount image /proc/self/fd/5: failed to mount squashfs filesystem: input/output error

Can anybody help?

Appreciated

[Justin Wang]

Support on this TVB-UKBB issue can be found on the pipeline's GitHub repository here:

https://github.com/McIntosh-Lab/tvb-ukbb/discussions/183