Open michellewang opened 3 months ago
Alternative: follow abstractions/"steps" listed in the slides
curation
processing
tracking
extraction
analysis
etc.
- Maybe also run
git init
if the user has Git installed
related to this:
I already have the cohort creator turning the nipoppy "hierarchy of folders" into a datalad sub-datasets with a code diretory.
Maybe this could be an option of the init CLI to create datalad datasets if datalad is installed and if requested by the user.
Just discussed this again with @nikhil153 and @mathdugre:
nipoppy init
which will attempt to run git init
in the code directory (which will now be inside the study directory, to be closer to BIDS)
From a discussion with @nikhil153 today.
DATASET_ROOT
and aCODE_ROOT
(for example). The code directory should have a structure that mirrors the dataset structure, except they should contain code/scripts instead of data:tabular
: for manifest-generation, tabular bagel generationdicom_reorg
: for wrangling raw, pre-BIDS imaging dataanalysis
: for downstream analysesrequirements.txt
file pre-populated with Nipoppygit init
if the user has Git installedI think the idea would be that this is a starting point for "good practices", but that users are not obligated to use these directory names exactly. Unlike the dataset layout which is mandatory since the Nipoppy tools expect it.