Sequence

• Look-Locker T1 mapping sequence

Convert image format

• MRI Convert: converting DICOM on Bruker ClinScan/Siemens Trio to Analyze (*.img) or Nifti (*.nii) format.
• fdf2img.m: converting Varian FDF format to Analyze.
• readVarianInfo.m: read Varian data acquisition info from procpar file.
  

Data Analysis

FACT: Functional MRI Analysis and Clustering Tools

ImageJ plugins for MRI analysis

• DCE-MRI Perfusion analysis: TOPPACT plugin
  
• MRI & fMRI analysis (including T1 mapping of IR data): QuickVol II plugin
  

DTI Analysis

• MedINRIA
• DTI Studio -- by Susumu Mori's lab at Johns Hopkins Univ.
• DSI Studio -- Includes DTI, DSI, Q-ball reconstruction and fiber tracking; by Isaac Tseng's lab at National Taiwan Univ

• Varian data
• T1 fit of FSE-IR-T1map
• T1 fit of Look-Locker-T1map
  
• T2 fit of MEMS-T2map
• ClinScan data
• T1 fit of multi-scan IR-SE
• T2 fit of multi-echo SE

Cardiac Analysis

• Segment

Atlas

Rat brain atlas

• Rat brain template (Karolinska Institutet, Sweden)
  

Mouse brain atlas

• Allen Brain Atlas
• Allen Brain Explorer
• 3D MRI Atlas Adult C57BL/6J Mouse Brain (Brookhaven National Lab, USA)
  
• Mouse MRI Atlas (Mouse Imaging Center, Toronto Centre for Phenogenomics)
• includes Variational Brain Atlas, Cerebral Vascular Atlas, & Neuroanatomy Atlas of the C57Bl/6j Mouse