Hi Joe
do you know what the forward model for VIBE is? mri_ms_fitparms uses the FLASH forward model of image formation then does a max likelihood estimation of the T1/T2*/PD using that model. If VIBE is a different model then it certainly won't work.
cheers Bruce
On Sun, 5 Jan 2020, joe vanderlo wrote:
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Dear Freesurfer community,
I computed T1 maps from Siemens VIBE (a spoiled 3D GRE variant; instead of Siemens FLASH (RF-Spoiled GRE)). I utilized mri_ms_fitparms to compute the T1 map (which looks ok) and compared the result to a T1 map (inline) from MP2RAGE. However, T1 values based on Siemens VIBE (FA: 4, 8, 13, 21, 34) are much lower than from MP2RAGE:
(results from the same subject, same day/position/setup scan, same ROIs)
WM/Corpus callosum: 652 ms (VIBE) vs 859 ms (MP2RAGE) Cerebellaer WM: 583 ms vs 834 ms
GM/Cortex: 845 ms vs 1184 ms Deep/Inner GM: 780 ms vs 920 ms
Liquor: 2222 or 3121 vs 2758 or 3652 ms Eye-Bulb: 112 vs 588
The literature suggests (mouse brain, 3T): Corpus callosum 1108±9 Internal capsule 913±16 Hippocampus 1310±15 Cortex 1246±28 (DOI: 10.1118/1.2968092)
The literature suggests (rat brain, 3T): WM: 1084 or 1110 ms GM: 1820 or 1470 ms (DOI: 10.1002/mrm.20605)
However, it appears that T1 values can be quite different (Fig. 3 from 10.1002/mrm.21313)
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Therefore, I would like to ask:
(1) Is it to be expected that T1 values differ dependent on the method used at same field strength and same scanner/setup?
(2) Considering that mri_ms_fitparms has not option for B1 correction, can I "optimize" the maps in a different manner? Would it make sense to run N4B on the respective VIBE scans (before map computation) or maybe directly on the T1 map?
(3) I would assume that the application of the VIBE sequence should be acceptable. Are there reasons not to believe so?
Thanks in advance