Bi-exponential fit using Java Image

This protocol uses the Java Image (JIM) software, installed on the MUSC CAIR hornet server, to perform a pixel-wise bi-exponential fit to image data, with the primary aim of extracting bi-exponential T₂ decay information.

There is a detailed on-line manual for JIM at the Xinapse web site. Follow the links for Image Analyze Software, then On-Line Manual. In the left frame, select chapter 12 Image Fitting, then work your way through the sub-section in the lower left frame.

• On the hornet server, convert the DICOM data to Analyze or NIFTI format. These instructions assume that conversion was performed using the dtoa software, as this includes the TE used for each image in the description line of the Analyze or NIFTI header. However, images converted to Analyze or NIFTI using other software can also be used, so long as you have another route to determine the TE for each image (e.g., noting the TEs used at scan time, or viewing the associated DICOM headers).
• If the Analyze files were produced using dtoa then cd to the subdirectory containing these images and type

  showana *.hdr | grep desc

  This displays a list of Analyze files and the description line from each header, which should contain the TE of the data in each file. If NIFTI files are being used instead, type

  showana *.nii* | grep desc

• To run JIM on the hornet server, you need to connect using the VNC method (as described under the Documentation / Informatics section of the MUSC CAIR Sharepoint website).
• Type jim & to start the software.
• Select Toolkits / Image Least-Squares Fitter.
• Fit function. y= S0a * exp( - TE / T2a ) + S0b * exp( - TE / T2b )
• Independent variable name TE
• Enter the remaining parameters as below. Under the Input Images section, click Add Image once for each echo time used. The JIM file browser can take some practice to use well; in particular it is usually safest to click the 'browse folder' icon and select the file graphically rather than type in the filename. Also, when browsing through subdirectories using the JIM file browser, double clicking on the folder icon immediately to the left of the filename is more successful than double clicking on the filename itself. The same holds when selecting the Output folder (i.e., use the graphical file browser).
  
• Click Apply to start the fit.
• To create a ratio of some of the fitted parameters, e.g. a ratio of S0b to S0a saved into file Sratio, fslmaths may be used, e.g.,

  fslmaths biS0b -div biS0a -nan -thr 0 Sratio