To execute workflows

[emanuelkessler]

What do you mean by 4. Run ?

[agahkarakuzu]

It means what follows, i.e., the execution of two nextflow workflows:

I also see that you requested access to data shared on OSF, which is already publicly available:

If you browse through files (under the files box), you'll land on the page above if you click /OSF Stograge/ds-bids/sub-phantom/sub-phantom.zip, then download (click 3 dots on the upper right).

Extract sub-phantom in a folder, then nextflow run venus-process-phantom.nf --bids /parent/folder/of/sub-phantom.

For in-vivo data, we have internal access currently due to our IRB ethics, but we are trying to make that part shareable as well. Either case, paper-analyses presented at https://qmrlab.org/VENUS uses first-order derivatives (i.e., the outputs of nextflow runs), which are publicly accessible at /OSF Storage/ds-bids/derivatives.zip.

[emanuelkessler]

Thanks a lot. Could have figured that out myself. Managed to execute the phantom sample.
Not quite sure what to do with the results, but I keep trying.

[agahkarakuzu]

No worries, I am glad that you were able to execute the phantom pipeline!

From my perspective, you independently replicated our results that have already been published in our MRM article, which, at least to me, is more exciting than receiving a citation on this paper, so thank you for that!

From your perspective, the same pipeline could be useful if you are interested in a similar analysis with the ISMRM/NIST system phantom. Say, you collected data from multiple scanners and would like to compare T1 accuracy. In that case, you would bidsify your data, and run the same workflow. It is also possible that you are interested in a different analysis with this data, which you already know how to process!