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.

MIDAS Installation


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MRISEG – Tissue segmentation – Superseded by IDLSEG.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

 

 

 

Last updated May 2021