Add exact commands used to run data

Question

Add exact commands used to run data

Closed this issue 3 months ago · 9 comments

It would be good to add the exact commands used to prep the data in the collection through the abcd-dicom2bids, the abcd-hcp-pipeline, and the functional connectivity code (for the connectivity matrices). This way not only are the repositories existent, but good example commands are existent and repeatable here too.

Answer 1 · 2021-09-29T21:24:39.000Z

Thanks @ericearl. Are you suggesting that the exact commands are listed in this repo or that they are documented in the readthedocs?

Answer 2 · 2021-09-29T21:27:50.000Z

Yes, the readthedocs, thanks!

Answer 3 · 2021-09-29T21:28:53.000Z

Sounds good! We will work to add that after this round of uploads. It won't be a high priority item, but we will hopefully get this in there by the end of the year.

Answer 4 · 2022-05-31T18:47:29.000Z

@ericearl do you have the exact commands on hand that you would like inserted into the documentation? That would help us add this into the ReadTheDocs more easily.

Answer 5 · 2022-05-31T19:22:38.000Z

@arueter1 No, I don't have any handy. My recommendation is to get the commands or scripts which Audrey or Tim or Anders use to convert with abcd-dicom2bids, process with abcd-hcp-pipeline, and prep the connectivity data. Sort of a "how it was done" record all the way down to the command line or scripts.

Answer 6 · 2022-05-31T19:30:31.000Z

All good -- we have them and we'll update as part of a broader set of revisions ;)

Answer 7 · 2022-05-31T20:03:58.000Z

Sounds good! Maybe even just a "abcd_processing_utilities" repository you reference in the readthedocs might be enough.

Answer 8 · 2023-01-04T17:06:16.000Z

We are intending to make a general slurm/s3 repository in the future. This issue will be answered when that repository is available.

Answer 9 · 2024-08-13T22:02:47.000Z

we are moving away from using the NDA, so will not be maintaining this repository anymore in the near future