FSL-DESPOT

T1/T2 mapping utilities




Introduction

despot is a command-line utility which allows the processing and transformation of SPGR, IR, and SSFP images into quantitative T1/T2 maps. The tools expect images as they are produced by the DESPOT1 and DESPOT2 sequences. The tools can also take advantage of additional IR images to correct for coil inhomogeneties.

IR, SPGR 20, SPGR 4, T1-map
Figure 1: Illustration of the processing steps. The IR-SPGR (1) and SPGR images with flip angles: 20° (2) and 4° (3) were used to calculate the T1 map (4).

Referencing

Deoni S.C.L., Peters T.M., Rutt B.K. High Resolution T1 and T2 Mapping of the Brain in a Clinically Acceptable Time with DESPOT1 and DESPOT2. Magnetic Resonance in Medicine. 53: 237-241 (2005).

Deoni S.C.L., Rutt B.K., Peters T.M. Synthetic T1-weighted Brain Image Generation with Incorporated Coil Intensity Correction using DESPOT1. Magnetic Resonance Imaging 24: 1241-1248 (2006).


A call to the "despot" program takes the following form:

despot [ListOfParameters]

Description of parameters

Parameters for input data

  • --d1=[spgr_data] (necessary for despot1 - optional for despot2)
  • --d2=[ssfp_data] (necessary for despot2)
  • --ird1=[ir_data] (necessary for b1-mapping in despot1-hifi)
  • --mask=[maskfile] (brain mask)
  • --t1=[t1file] (t1 map as an input for despot2 - compulsory if no spgr data are provided)
  • --b1=[b1file] (b1 map as a multiplicative factor for flip angles used in despot1-hifi)

    Parameters for other inputs

    Repetition times
  • --tr1=[value] (repetition time for spgr data - output T1 maps will be in the same units)
  • --tr2=[value] (repetition time for ssfp data - same units as output T2 map)
  • --irtr=[value] (repetition time for ir data - same units as tr1)
    Flip angles
  • --fa1=[textFile] (ascii text file containing the flip angles of spgr data - in degrees)
  • --fa2=[textFile] (ascii text file containing the flip angles of ssfp data - in degrees)
  • --irfa=[textFile] (ascii text file containing the flip angles of ir data - in degrees)
    HIFI-specific inputs and fudge factors
  • --ti=[textFile] (ascii text file containing the inversion times for ir data - same unit as repetition times)
  • --nrf=[value] (number of RF pulses for ir-spgr data)
  • --tifudge=[value] (multiplicative fudge factor for ti - default=1.0)
  • --m0fudge=[value] (multiplicative fudge factor for M0 - default=1.0)
  • --effectiveinversion=[value] (effective inversion angle in degrees - default=180.0)
    Other options
  • --out=[basename] (output basename - example output will be [basename]_despot1_t1map if despot1-mode chosen - default="despot")
  • --mode=[value] (available modes are: despot1, despot2, despot1_hifi and mcdespot
  • --wls (weighted least-squares in despot1 and 2. increases the robustness of the fit)
  • --verbose (switch on diagnostic messages)
  • --help (print out help message)


    Copyright © 2000-2009, University of Oxford. Written by S. Jbabdi and J. Scholz