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neurolabusc avatar neurolabusc commented on August 16, 2024

A T2_FLAIR should be labeled FLAIR in the BIDS specification. In T1-weighted scans fluid (CSF) is intrinsically dark. In T2-weighted images fluid is intrinsically bright unless a precise inversion time is used to knock out the fluid signal. The resulting image is sometimes referred to as "T2 FLAIR", "FLAIR" or (if you use Siemens) "dark fluid". In BIDS, T2 refers to a conventional T2 image and FLAIR refers to a T2-FLAIR. The contrast of a FLAIR image is different than T2, so processing such as normalization with an intra-modal cost function will fail if the FLAIR is treated like a T2.

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