PRISM Studio Overview

PRISM Studio is the web-based interface for PRISM. It provides a user-friendly way to manage projects, convert data, validate datasets, and run scoring recipes.

Launching PRISM Studio

python prism-studio.py

Your browser opens to http://localhost:5001. If it doesn’t open automatically, navigate there manually.

Daily health checks (repo root):

# fast sanity check
bash scripts/ci/run_local_smoke.sh

# full required gate
bash scripts/ci/run_runtime_gate.sh

Home Page

The home page shows:

  1. Current Project – The active project (if loaded)

  2. Quick Actions – Common tasks

  3. Recent Projects – Previously opened projects

  4. Getting Started – Links to documentation and workshop

Projects Page

Create New Project

Creates a YODA-structured project:

project_name/
├── dataset_description.json
├── participants.tsv
├── sub-001/
│   └── ...            ← PRISM validates here
├── code/              ← Your analysis scripts
├── analysis/          ← Results and derivatives
├── project.json       ← Project metadata
├── contributors.json  ← Team information
└── CITATION.cff       ← Citation file

Fields:

  • Project Name: Folder name (no spaces, use underscores)

  • Project Location: Parent directory

Open Existing Project

Load a project by selecting its project.json file or the project folder.

Recent Projects: Click any recent project to quickly reopen it.

Project Metadata

Once a project is loaded, you can edit:

  • Dataset Description – Name, authors, license

  • Participants – Demographic variables, NeuroBagel compliance

  • Settings – Library paths, default modalities

Validator Page

Running Validation

  1. Your project folder is pre-selected

  2. Click Validate

  3. Wait for results (progress shown)

Understanding Results

Results are grouped by severity:

Icon

Level

Meaning

❌

Error

Must fix – dataset is invalid

⚠️

Warning

Should fix – may cause issues

💡

Suggestion

Could improve – best practices

Result Details

Click any issue to see:

  • File path – Which file has the problem

  • Error code – e.g., PRISM101

  • Description – What’s wrong

  • How to fix – Suggested solution

Auto-Fix

Some issues can be fixed automatically:

  1. Click the Auto-Fix button on fixable issues

  2. Review the proposed changes

  3. Apply fixes

BIDS Validation

Toggle Include BIDS Validation to also run the standard BIDS validator. This checks MRI-specific requirements.

Converter Page

Supported Formats

Format

Extension

Notes

Excel

.xlsx, .xls

Multiple sheets supported

CSV

.csv

Comma-separated

TSV

.tsv

Tab-separated

SPSS

.save

With value labels

LimeSurvey

.csv

Special handling for LS exports

Conversion Workflow

  1. Select Source File – Browse or drag-and-drop

  2. Preview Data – Check columns and rows

  3. Map Columns:

    • Select the participant ID column

    • Choose which columns to include

    • Set the task name

  4. Convert – Generate PRISM-formatted files

  5. Save to Project – Copy files to your project dataset root

Participants Mapping

For demographic data with custom encodings:

  1. Click Participants Mapping

  2. Define transformation rules

  3. Apply to generate standardized participants.tsv

See Participants Mapping for details.

Tools

File Management

Renamer by Example: Quickly rename files to PRISM/BIDS format.

  • Enter an example: participant_001_task.tsv → sub-001_task-depression_survey.tsv

  • Apply the pattern to all similar files

Folder Organizer: Move flat files into subject/session/modality folders.

Survey Export

Survey Generator: Create survey files from scratch or templates.

Survey Customizer: Modify existing surveys:

  • Add/remove items

  • Edit response options

  • Update translations

Library Browser: Browse the official PRISM survey library with 100+ validated instruments.

Recipes & Scoring

Recipe Runner:

  1. Select your dataset

  2. Choose recipes (scoring algorithms)

  3. Run to calculate scores

  4. Export as SPSS (.save) or CSV

Recipe Features:

  • Sum scores, mean scores, reverse coding

  • Conditional scoring (subscales)

  • Custom formulas

  • Value labels for SPSS

Template Editor

Create and edit survey/biometrics metadata templates:

  • Items: Questions, response options

  • Bilingual: German and English text

  • Schema Validation: Ensures templates are valid

Keyboard Shortcuts

Shortcut

Action

Ctrl/Cmd + S

Save current file

Ctrl/Cmd + O

Open project

Ctrl/Cmd + V

Run validation

Quitting PRISM Studio

Click Quit in the navigation bar (red X icon) to:

  1. Save any unsaved changes

  2. Shut down the web server

  3. Close the application

Or press Ctrl+C in the terminal where PRISM Studio is running.

Next Steps