3DiCSI 1.9.11

Analyze CSI data fast and easy.
3DiCSI - The main window of 3DiCSI enables you to select the file to analyze.
  5 Screenshots
3DiCSI is a small, simple, easy to use application developed to help you interpret Chemical Shift Imaging (CSI) data.

It combines data visualization, spectral processing, spectral localization and estimation, spectral quantification together with multi-variate analytical procedures, such as Principal Component Analysis (PCA) and constrained Non-negative Matrix Factorization (cNMF).

In particular, cNMF provides an efficient way to recover underlying spectral patterns that are physically meaningful.

Main features:

  • Data Input and Visualization:
  • Automatic importation of 1D/2D/3D CSI raw data from Philips, GE, Siemens and Bruker scanners.
  • Any unknown data type can be imported by manually entering parameters.
  • Any additional formats are also supported through third-party plug-ins.
  • CSI data and anatomic reference images are registered and displayed in the same window.
  • Each voxel is displayed in a separate window, its spatial location clearly visualized in the three orthogonal image windows.
  • 3D image reconstruction from images in one orientation.
  • Multi-dimensional Spectral Data Processing:
  • Constant phase and linear phase correction.
  • Temporal filtering ( Lorentzian, Gaussian, or combined).
  • Spatial smoothing ( Hamming, Cosine, Fermi).
  • Baseline correction.
  • Water suppression.
  • PPM origin adjustment and zero filling.
  • Lipid Suppression.
  • Peak alignment.
  • Batch Processing:
  • Sequence of processing steps can be recorded in a macro file and applied to the CSI data set.
  • The same macro file can be applied to a series of exams in a batch mode.
  • Spectral Localization:
  • Real-time mouse-facilitated interactive voxel shifting in all 3 dimensions.
  • Averaging of selected multiple voxels.
  • Spectral estimation of a user drawn 2D/3D region of interest.
  • Multi-variate spectral analysis:
  • Principal Component Analysis (PCA) for user defined spectral region and ROI, to identify Principal Components (PCs) for the variation sources contained in the CSI data set.
  • PCA-based iterative peak align procedure to remove frequency and phase variations.
  • Constrained Non-Negative Matrix Factorization (cNMF) method to recover spectral patterns and their spatial distributions that are physically meaningful.
  • Spectral Quantification:
  • Metabolic map generation using area integration and PCA.
  • Map generation for peak ratio and for user defined regions.
  • Absolute quantification of metabolite concentration using reference spectrum.
  • Map display scale adjustment to enable comparison between different sets.
  • Spectral integration with user-controlled baseline correction.
  • Data Output:
  • Various result output options, such as HTML format report, CSI slice and image print out, display copy and paste functions, spectral ascii/binary exportation, metabolic image exportation.
  • Program extensibility:
  • Plug-in mechanism to support CSI data importation module developed by third-party.

last updated on:
February 19th, 2011, 10:29 GMT
file size:
3.3 MB
license type:
developed by:
Qi Zhao
operating system(s):
Windows All
C: \ Science / CAD
Download Button

In a hurry? Add it to your Download Basket!

user rating



Rate it!
5 Screenshots
3DiCSI - To add an exam you will use the Project menu.3DiCSI - To adjust the colors you will access the Map menu.3DiCSI3DiCSI

Add your review!