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Quick Start

This guide walks you through importing and processing your first dataset with NILS.

Overview

A typical NILS workflow consists of:

  1. Import - Load DICOM data into the system
  2. Classify - Automatically identify sequence types
  3. Sort - Organize files into a structured hierarchy
  4. Anonymize - De-identify patient information
  5. Export - Convert to BIDS format (optional)

Step 1: Access the Dashboard

After starting NILS, navigate to http://localhost:5173. You'll see the main dashboard:

Dashboard

Step 2: Import DICOM Data

  1. Click Import in the sidebar
  2. Specify the path to your DICOM folder
  3. Click Start Import

NILS will scan the folder and extract metadata from all DICOM files.

Supported Formats

NILS supports standard DICOM files (.dcm) and files without extensions.

Step 3: Review Classification

After import, NILS automatically classifies each series:

  • Navigate to Database to view all imported series
  • Each series shows its detected sequence type (T1w, T2w, FLAIR, etc.)
  • Review and correct any misclassifications if needed

Step 4: Create a Cohort

Cohorts help organize subjects for processing:

  1. Go to Cohorts → New Cohort
  2. Enter a name and description
  3. Add subjects from the database
  4. Save the cohort

Step 5: Run Sorting Pipeline

  1. Select your cohort
  2. Click Sort in the pipeline steps
  3. Configure output directory
  4. Start the sorting job

Monitor progress in the Jobs tab.

Step 6: Anonymization (Optional)

To de-identify data:

  1. Select sorted data
  2. Click Anonymize
  3. Review the anonymization profile
  4. Run the anonymization job

Step 7: BIDS Export (Optional)

Export to BIDS format:

  1. Select anonymized data
  2. Click BIDS Export
  3. Configure BIDS metadata
  4. Export

Next Steps