FSL on RETZ

From SBIwiki

Jump to: navigation, search

Receive coil array bias field removal in FSL after 32 ch array NOVA at 3T.

With 32 ch ( actually with 8 ch array as well) use the same pad thickness under the head all the time to keep the same distance between the occipital lobe and the coil!

Summary: T1w 3D data after 8 ch. array in-Vivo are more or less immune to the chosen smoothing distance ( 20-50 mm) , default is 20 mm.

T1w 3D data after 32 ch. coil is more sensitive and converge to the results obtained after 8 ch. if the smoothing distance is (FWHM) 50 - 60 mm.

Intensity range after 32 ch. is compressed ( see histogram) two times compare to 8 ch. This may affect the segmentation in other packages, but not in FSL since FSL does not use prior-knowledge in segmentation. If this is an issue the T1w image after bias field removal can be scaled up ( multiplied by 2) or study template with prior knowledge must be created.

Ref. Quantitative Evaluation of Intensity Inhomogeneity Correction Methods for Structural MR Brain Images., Marco Ganzetti, Neuroinform., 2016


File:Nova-inVivo 30mm smooth.jpg


File:Nova-inVivo 50 mm smooth.jpg


File:Nova-inVivo_hist_30mm_smooth.jpg



File:Nova-inVivo segment.jpg


File:Nova-inVivo pve.jpg

Personal tools
MEG