FITMAN Chapter 1.2 - dwong263/MAGIQ GitHub Wiki

Preprocessing Lineshape Correction

Background

MR spectra must be converted from vnmr (vnmrJ) format to fitMAN format. In addition MR spectra normally contain lineshape distortions due to eddy currents, gradient coil vibration, and B0 inhomogeneity, that distort the pure Lorentzian lineshape that is normally expected in NMR. Since the fitting procedure used for spectral quantification incorporates a Lorentzian lineshape, it is best to restore the Lorentzian lineshape of the spectrum prior to quantification.

Implementation

Conversion of 4T vnmrJ format spectra, GE format spectra, and Siemens format spectra to fitMAN format is accomplished by several C++ programs found in the folder fitman/bin/<OS>/:

  1. 4T vnmrJ to FITMAN: 4t_cv
  2. GE to FITMAN: ge2fitman
  3. Siemens to FITMAN: sim2fitman

These programs can be executed from the command line or through the fitMANSuite program.

Command Line

4t_cv

Type 4t_cv to see the usage options.

4t_cv version 1.0
Copyright (C) 2000-2006 Robarts Research Institute
                        Imaging Research Laboratories

Usage: 4t_cv in_file out_file
<-scale> <-scaleby scale_factor> <-bc> <-zf #_points>

<-ecc> reference_file
<-scale> <-scaleby scale_factor> <-bc> <-zf #_points>

<-quality> delay_time(us) reference_file
<-norm> <-scale> <-scaleby scale_factor> <-bc> <-zf #_points> <-f FWHM>

<-quecc> QUALITY_points(real+imag) delay_time(us) reference_file
<-norm> <-scale> <-scaleby scale_factor> <-bc> <-zf #_points> <-(i)f
FWHM>
Note: <-if> must be specified for suppressed and unsuppressed file
separately

WARNING: Filtering applied with negative delay time assumes data is an
echo.

To convert the vnmrJ spectrum to fitMAN format and complete lineshape correction with QUECC, type something similar to the following:

4t_cv full_spectrum_filename.fid converted_filename –scale –bc –if –quecc 400 500
full_water_reference_filename.fid –norm –scale –bc –if

ge2fitman

Type ge2fitman to see the usage options.

Usage:
>> ge2fitman [-options] in_file [-in_file_options] ...
             [reference_file] [-ref_file_options] out_file

   -options:
       -h, -help, -nv, -ow, -ver

   -in_file_options:
       -scale /or/ -scaleby scale_factor, -bc,
       -if, -bs, -nbs, -ir, -irn
       -(ecc /or/ ...
         quality delay_time(us) /or/ ...
         quecc quality_points(real+imag) delay_time(us))
         reference_file

   -ref_file_options:
       -rscale /or/ -rscaleby scale_factor, -rbc, -f filter_factor,
       -rif, -rbs, -rnbs, -norm

sim2fitman

Type sim2fitman to see the usage options.

Usage:
>> sim2fitman [-options] in_file [-in_file_options] out_file

   -options:
       -h, -help, -nv, -ow, -ver

   -in_file_options:
       -scale /or/ -scaleby scale_factor, -bc,
       -if, -bs, -nbs

fitMAN Suite

In the fitMAN Suite, select: File > Convert Raw Data

  1. Select output file name
  2. Select Input file (click into directory if browsing). For Varian, select directory (*.fid)
  3. Select: Use Baseline Correction, Auto Filter, QUECC
  4. Select water reference file. For Varian, select directory (*.fid)
  5. Select: Use Baseline Correction, Normalize, Auto filter
  6. Enter Delay time and number of points at the beginning of FID to perform QUALITY deconvolution

Output

In both cases, either command line implementation, or fitMANSuite implementation, two files will be generated:

  • Converted_filename_s.dat: contains the water suppressed spectrum
  • Converted_filename_uns.dat: contains the water unsuppressed spectrum
⚠️ **GitHub.com Fallback** ⚠️