TVB-ukbb installation on MacOS

[michefabb]

Dear all, I have posted this also on the TVB Users Google forum at https://groups.google.com/g/tvb-users/c/7Rkj6x9Lqjs , I repost it here hoping a help!

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 errors 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.

UPDATE OF TODAY

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?

[pmahon3]

Hey @michefabb,

We are looking into this.

In the mean time: the pipeline is well tested on linux (this may be a mac support issue) so if it is blocking your work and you have access to a linux machine or can run a linux virtual machine on your mac try to proceed that way.

Will keep you updated.

[michefabb]

@pmahon3
Dear Patrick,

I greatly appreciate your support! I have used Vagrant to launch Syngularity on a Linux VM on my Mac (Intel Silicon), but I received the error above…

Feel free to let me know if you need any further information from my side.

Thanks again and looking forward,

Michelangelo

[pmahon3]

Thanks Michelangelo. That's useful info

[michefabb]

@pmahon3
Dear All,

I would kindly ask you if you have any feedback to the above.
I did not mention explicitly that the Singularity installation website https://docs.sylabs.io/guides/3.2/user-guide/installation.html#mac mandates MacOS users to use Vagrant to launch Singularity containers, reason why I am using this latter as VM.

Hope it helps,

Miche

[pmahon3]

Hey @michefabb,

I'm currently working from a windows machine but will have a mac soon, unfortunately the order was delayed. Should have an update on this by the end of the month.

Patrick

[michefabb]

@pmahon3 thank you very much, really appreciated!

PS unfortunately it looks I cannot use the EBRAINS TVB-Image Processing Pipeline https://wiki.ebrains.eu/bin/view/Collabs/tvb-pipeline/ since my MRI data do not include the fieldmap as needed from this latter...would you have any suggestion / workaround in the meanwhile? :)