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Metabolite Imaging and Data Analysis
Software
List of Documents
Getting Started
MIDAS_Introduction: A brief overview of the MIDAS project.
MIDAS_Overview: An Overview of MRI and MRSI processing functions in MIDAS.
MIDAS_Tutorial: A comprehensive tutorial of the MIDAS processing.
EPSI_Processing_Introduction: Processing for the volumetric EPSI data.
Help Files
MIDAS FAQ - Frequently Asked Questions
AutoMask – Automated brain and lipid mask creation tool.
Batch Processing - Pipeline processing of multiple studies.
DNPCA – Spectral denoising using PCA
EPSI2 – Preprocessing for EPSI data.
FDFT – MRSI Reconstruction.
FITT – Automated parametric spectral analysis.
FITT2 – Changes in v2.
IDLSEG – Tissue
Segmentation
IMCALC – Image calculation
IMPORTER – Project management and data import.
LITE – Lipid k-space extrapolation.
METAFIT – Wrapper for iterative FITT
MIDASTools – Button-bar for running MIDAS.
MINT – ROI spectral integration and analysis
MRMask – Brain and Lipid masks from MRI and segmentation.
MRISEG – Tissue segmentation – Superseded by IDLSEG.
MSREG – Affine registration between image series.
PRANA – Project Review and Analysis.
QMAPS – Simple quality evaluation of FITT results.
QUID – Display using mosaic format
RefDat - B0 and ECC map formation.
Registration – Spatial registration functions.
SID – MRI and MRSI display.
SINorm – Signal normalization of fitted metabolite images.
SVS – Single Voxel Spectroscopy processing tools.
TIMO – T1 and M0 calculation (still under development)
TMAP – Temperature mapping
Utilities – Miscellaneous utility functions.
Viewer – MRI and MRSI display.
Volumizer – Data organizer.
ZipStudy – Copy study data and compress.
Additional Utilities and Other Information
MIDAS_Delete_Nodes – Delete data and restore to initial processing. See Tutorial.
MIDAS Signal Calibration – Calibration procedure required for SINorm
Analyze_Import_Export – IDL utility and function description for Analyze format I/O
MakeSIData – Program for simulation of MRSI data.
XMLCompare – Utility to compare subject.xml files
VESPA - Spectral simulation using GAMMA (Courtesy B. Soher, available separately).
MIDAS Server - Web-based image server supporting the MIDAS Viewer.
Notes - Processing segmentation images for brain lesion studies.
Detailed Implementation and Developer Information
MIDAS_Project_Description - this is the main project definition file.
MidasLibrary – Programmer documentation
MidasParameters
– List of parameter definitions
Agreements
Information on distribution of the EPSI sequence and the MIDAS software is provided on the FAQ page.
Links to Other Tools and Packages Used
MIDAS – Project home page
IDL – Image Display Language from Harris
FSL – Includes FAST – a segmentation program used in MIDAS
BrainWeb – Simulated MRI data from Montreal Neurological Institute
MRIcro – Display for Analyze files from Chris Rorden
Rview – Full featured display from Colin Studholme
ImageJ – Java display from NIH
MIPAV – Image display
Notepad++ – Text editor, convenient for editing XML files.
TortoiseSVN – Source code control system used for MIDAS
7-zip – compression utility used in ZipStudy