cmind-py User Manual

This page contains details of the processed data files that are available in the C-MIND database as well as a few examples of data processing using files obtained from the database.

Installation

• Installation
  • Downloading
  • Installation from source
  • Specifying Pediatric Template Locations
  • Setting Up the Environment
  • Dependencies

CMIND Pipeline Details

• Structural Processing
  • Defacing Structural Volumes
  • Structural Preprocessing
  • Segmentation
  • Registration to the Study Template
  • Normalization to MNI space
• CBF and T1 map Processing
  • CBF preprocessing
  • T1 estimation preprocessing
  • T1 map fitting
  • Coregistration of T1map and CBF volumes
  • Registration to Structural Space
  • CBF quantification
  • Normalization to Standard Space
• ASL/BOLD fMRI Processing
  • Motion Correction
  • fMRI Preprocessing
  • Outlier Detection
  • First-level GLM
  • Registration to Structural Space
  • Normalization to Standard Space

Software Usage

• Command Line Usage
• Calling Functions From Within Python
• Usage in LONI
• Using with Nipype

Database Outputs

• Database File Variables
  • Raw
  • Structural Processing
  • DTI/HARDI Processing
  • Physiological Processing
  • Functional Processing
    • Contrasts
    • Behavioral Responses

Example usage of C-MIND processed data

• DTI/HARDI Processing
  • QC Data files
  • DTI Toolkit: obtaining FA, ADC and tensor information via dti_recon
  • DTI tractography using DTI Toolkit
  • HARDI/ODF tractography using DTI Toolkit
  • FSL’s dtifit: obtaining FA, ADC and tensor information
• Simultaneous ASL/BOLD Processing
  • ASL/BOLD Data files
  • Setting up a second level analysis

References

• Citations

Indices and tables

• Search Page