Add exact commands used to run data

[ericearl]

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.

[arueter1]

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

[ericearl]

Yes, the readthedocs, thanks!

[arueter1]

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.

[arueter1]

@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.

[ericearl]

@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.

[ericfeczko]

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

[ericearl]

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

[audreymhoughton]

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

[LuciMoore]

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