Khan Lab Folder Structure

This document outlines the proposed organized folder structure for our neuroimaging lab under /projects/<labnumber>/khanlab. This structure is designed to centralize data, streamline collaboration, and ensure consistency across all projects. This structure aims to improve collaboration, data accessibility, and lab productivity. For questions or feedback, contact the lab manager.

Root Directory

All lab-related data and projects are organized under:

/projects/<labnumber>/khanlab

Top-Level Directories

| Directory               | Purpose                                                                                  |
|-------------------------|------------------------------------------------------------------------------------------|
| `/datasets`             | Raw and processed datasets, organized by source (internal, external, aggregated).        |
| `/trainees`             | Individual folders for lab members (current and past).                                   |
| `/code`                 | Central repository for lab-wide code, scripts, and pipelines.                            |
| `/docs`                 | Documentation files (e.g., dataset metadata, user guides, README files).                 |

Datasets Directory

All datasets are stored in the /datasets directory, with raw and processed data grouped by dataset.

/datasets
    /internal        # Datasets generated within the lab
        /<dataset_name>
            /sourcedata        # Raw source
            /tabular           # Tabular data
            /bids              # BIDS (raw or minimally-preproc)
            /derivatives       # Processed data from pipelines (e.g., fMRIPrep, QSIprep)
            /code              # Dataset-specific code
            /logs              # Logs from processing or analysis steps
    /external        # External datasets (e.g., HCP, UK Biobank)
    /aggregated      # Combined datasets or multi-dataset studies

Trainees Directory

Individual folders for lab members, divided into current and past trainees. These folders should store the data that you wish to retain (e.g. analyses related to papers published or in-progress). These folders will inherit group-writable permission so that lab managers can move/archive the data at a later date.

What about my folders in /project//?

These folders (one for each allocation, including default allocation and project allocations, should not be used for any persistent data, since the lab managers do not have access to them for archiving, nor do your fellow lab members (for collaboration). These folders will be wiped after you leave the lab.

/trainees
    /current
        /<username>
            /<project_name>
    /past
        /<username>
            /<archived_project_name>

Code Directory

Centralized location for shared scripts, code, containers required by the group. This folder should be group-writable by default.

/code
  /containers

Docs Directory

Documentation related to datasets, projects, or lab processes.

/docs
    dataset_guide.md
    pipeline_instructions.md
    lab_policies.md

Folder Creation Guide

When adding new data or projects:

1. For Datasets:
   • Create a folder under /datasets/internal or /datasets/external.
   • Use subfolders for sourcedata, bids, tabular, derivatives, code.
   • Ideally, raw data should be placed in sourcedata, and the code to generate the other folders should be in a github repository and cloned in code.
2. For Trainees:
   • Create a folder under /trainees/current/<username>.
   • Archive past members under /trainees/past.
3. For Code:
   • Use github repositories under the khanlab org
   • Clone into relevant code subdirectories

Enforcing Structure

1. Use automated scripts to ensure directory consistency.
2. Periodically audit the structure to maintain organization.
3. Follow permissions guidelines to prevent unauthorized access.