config.yml

# Example config file for MP2RAGE-utils
# NOTE: LEAVE FIELDS EMPTY/BLANK IF NOT USED. DO NOT DELETE.

# Required input parameters (full path must be provided)
INV1: example/MP2RAGE_INV1.nii
INV2: example/MP2RAGE_INV2.nii
UNI: example/MP2RAGE_UNI.nii

# Optional input parameters (full path must be provided)
T1map: 
sa2rageINV2: example/Sa2RAGE_invContrast2.nii
sa2rageB1map: example/Sa2RAGE_B1map.nii
tflB1map:

# MP2RAGE parameters (from your protocol)
B0: 7.0 # Field Strength
TR: 6.0 # MP2RAGE TR
TRFLASH: 6.7e-3 # GRE readout TR
FlipDegrees: 4 5 # Flip angles
TIs: 800e-3 2700e-3 # Inversion times
SlicesPerSlab: 143
PartialFourierInSlice: 0.75

# Background removal options (1 = yes, 0 = no)
DenoiseUNI: 1
DenoiseT1map: 1
DenoiseWeight: 10

# Calculate additional maps (1 = yes, 0 = no)
CalculateT1map: 1
CalculateR1map: 1
CalculateM0map: 1

# B1+ correction (1 = yes, 0 = no), coregister requires SPM
B1correct: 1
Coregister: 0

# If B1+ correcting with Sa2RAGE, give parameters (from your protocol)
sa2rageTR: 2.4
sa2rageTRFLASH: 2.75e-3
sa2rageFlipDegrees: 4 10
sa2rageTIs: 47e-3 1800e-3
sa2rageBaseResolution: 128
sa2ragePartialFourierInPE: 0.75 
sa2rageiPATPhaseEncode: 3
sa2rageRefLines: 18
sa2rageAverageT1: 1.5