TY - JOUR
T1 - Optimizing parameter choice for FSL-Brain Extraction Tool (BET) on 3D T1 images in multiple sclerosis
AU - Popescu, V.
AU - Battaglini, M.
AU - Hoogstrate, W. S.
AU - Verfaillie, S. C.J.
AU - Sluimer, I. C.
AU - van Schijndel, R. A.
AU - van Dijk, B. W.
AU - Cover, K. S.
AU - Knol, D. L.
AU - Jenkinson, M.
AU - Barkhof, F.
AU - de Stefano, N.
AU - Vrenken, H.
AU - Montalban, X.
AU - Fazekas, F.
AU - Filippi, M.
AU - Frederiksen, J.
AU - Kappos, L.
AU - Miller, D.
AU - Palace, J.
AU - Polman, C.
AU - Rocca, M.
AU - Rovira, A.
AU - Yousry, T.
N1 - Funding Information:
This study was funded by the MAGNIMS/ECTRIMS Fellowship 2009 awarded to Veronica Popescu
Funding Information:
The MS Center Amsterdam is funded by the Dutch MS Research Foundation program grants 98–358 , 02-358b , 05-358c , 09-358d .
Funding Information:
Veronica Popescu is supported by the Dutch MS Research Foundation , grant no. 10-718MS .
PY - 2012/7/16
Y1 - 2012/7/16
N2 - Background: Brain atrophy studies often use FSL-BET (Brain Extraction Tool) as the first step of image processing. Default BET does not always give satisfactory results on 3DT1 MR images, which negatively impacts atrophy measurements. Finding the right alternative BET settings can be a difficult and time-consuming task, which can introduce unwanted variability. Aim: To systematically analyze the performance of BET in images of MS patients by varying its parameters and options combinations, and quantitatively comparing its results to a manual gold standard. Methods: Images from 159 MS patients were selected from different MAGNIMS consortium centers, and 16 different 3DT1 acquisition protocols at 1.5. T or 3. T. Before running BET, one of three pre-processing pipelines was applied: (1) no pre-processing, (2) removal of neck slices, or (3) additional N3 inhomogeneity correction. Then BET was applied, systematically varying the fractional intensity threshold (the "f" parameter) and with either one of the main BET options ("B" - bias field correction and neck cleanup, "R" - robust brain center estimation, or "S" - eye and optic nerve cleanup) or none. For comparison, intracranial cavity masks were manually created for all image volumes. FSL-FAST (FMRIB's Automated Segmentation Tool) tissue-type segmentation was run on all BET output images and on the image volumes masked with the manual intracranial cavity masks (thus creating the gold-standard tissue masks). The resulting brain tissue masks were quantitatively compared to the gold standard using Dice overlap coefficient (DOC). Normalized brain volumes (NBV) were calculated with SIENAX. NBV values obtained using for SIENAX other BET settings than default were compared to gold standard NBV with the paired t-test. Results: The parameter/preprocessing/options combinations resulted in 20,988 BET runs. The median DOC for default BET (f = 0.5, g = 0) was 0.913 (range 0.321-0.977) across all 159 native scans. For all acquisition protocols, brain extraction was substantially improved for lower values of "f" than the default value. Using native images, optimum BET performance was observed for f = 0.2 with option "B", giving median DOC = 0.979 (range 0.867-0.994). Using neck removal before BET, optimum BET performance was observed for f = 0.1 with option "B", giving median DOC 0.983 (range 0.844-0.996). Using the above BET-options for SIENAX instead of default, the NBV values obtained from images after neck removal with f = 0.1 and option "B" did not differ statistically from NBV values obtained with gold-standard. Conclusion: Although default BET performs reasonably well on most 3DT1 images of MS patients, the performance can be improved substantially. The removal of the neck slices, either externally or within BET, has a marked positive effect on the brain extraction quality. BET option "B" with f = 0.1 after removal of the neck slices seems to work best for all acquisition protocols.
AB - Background: Brain atrophy studies often use FSL-BET (Brain Extraction Tool) as the first step of image processing. Default BET does not always give satisfactory results on 3DT1 MR images, which negatively impacts atrophy measurements. Finding the right alternative BET settings can be a difficult and time-consuming task, which can introduce unwanted variability. Aim: To systematically analyze the performance of BET in images of MS patients by varying its parameters and options combinations, and quantitatively comparing its results to a manual gold standard. Methods: Images from 159 MS patients were selected from different MAGNIMS consortium centers, and 16 different 3DT1 acquisition protocols at 1.5. T or 3. T. Before running BET, one of three pre-processing pipelines was applied: (1) no pre-processing, (2) removal of neck slices, or (3) additional N3 inhomogeneity correction. Then BET was applied, systematically varying the fractional intensity threshold (the "f" parameter) and with either one of the main BET options ("B" - bias field correction and neck cleanup, "R" - robust brain center estimation, or "S" - eye and optic nerve cleanup) or none. For comparison, intracranial cavity masks were manually created for all image volumes. FSL-FAST (FMRIB's Automated Segmentation Tool) tissue-type segmentation was run on all BET output images and on the image volumes masked with the manual intracranial cavity masks (thus creating the gold-standard tissue masks). The resulting brain tissue masks were quantitatively compared to the gold standard using Dice overlap coefficient (DOC). Normalized brain volumes (NBV) were calculated with SIENAX. NBV values obtained using for SIENAX other BET settings than default were compared to gold standard NBV with the paired t-test. Results: The parameter/preprocessing/options combinations resulted in 20,988 BET runs. The median DOC for default BET (f = 0.5, g = 0) was 0.913 (range 0.321-0.977) across all 159 native scans. For all acquisition protocols, brain extraction was substantially improved for lower values of "f" than the default value. Using native images, optimum BET performance was observed for f = 0.2 with option "B", giving median DOC = 0.979 (range 0.867-0.994). Using neck removal before BET, optimum BET performance was observed for f = 0.1 with option "B", giving median DOC 0.983 (range 0.844-0.996). Using the above BET-options for SIENAX instead of default, the NBV values obtained from images after neck removal with f = 0.1 and option "B" did not differ statistically from NBV values obtained with gold-standard. Conclusion: Although default BET performs reasonably well on most 3DT1 images of MS patients, the performance can be improved substantially. The removal of the neck slices, either externally or within BET, has a marked positive effect on the brain extraction quality. BET option "B" with f = 0.1 after removal of the neck slices seems to work best for all acquisition protocols.
KW - BET
KW - Brain extraction
KW - FSL
KW - MRI
KW - Multiple sclerosis
KW - Segmentation
UR - http://www.scopus.com/inward/record.url?scp=84861781811&partnerID=8YFLogxK
U2 - 10.1016/j.neuroimage.2012.03.074
DO - 10.1016/j.neuroimage.2012.03.074
M3 - Article
C2 - 22484407
AN - SCOPUS:84861781811
VL - 61
SP - 1484
EP - 1494
JO - NeuroImage
JF - NeuroImage
SN - 1053-8119
IS - 4
ER -