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.

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