Hi, can any FSL expert please kindly give some lights on my problem below. Thanks.
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Hi all, as stated in the subject, I had a problem with FAST from fslvbm. I ran the command fast -R 0.3 -H 0.1 -v subjID_struc_brain on 160 subjects. About 100 of the subjects resulted an empty (all dark, intensity 0 for all voxels) subjID_struc_GM while some are ok.
The structural image is from multi-echo MPRAGE. And I used the brainmask from Freesurfer for FAST (this procedure work well for all MPRAGE images and some multi-echo MPRAGE images). Here are the output from FAST for one of the problematic subjects. For some other subjects, it gave nan for class 3 mean start from Tanaka iteration 0.
Any help is appreciated.
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Starting Single Image Segmentation
T1-weighted image
Imagesize : 256 x 256 x 256
Pixelsize : 1 x 1 x 1
1 3.95124
2 4.40672
3 4.63473
KMeans Iteration 0
KMeans Iteration 1
KMeans Iteration 2
KMeans Iteration 3
KMeans Iteration 4
KMeans Iteration 5
KMeans Iteration 6
KMeans Iteration 7
KMeans Iteration 8
KMeans Iteration 9
KMeans Iteration 10
KMeans Iteration 11
KMeans Iteration 12
KMeans Iteration 13
KMeans Iteration 14
KMeans Iteration 15
KMeans Iteration 16
KMeans Iteration 17
KMeans Iteration 18
Tanaka Iteration 0 bias field 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=1.5871e+07 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=1.59885e+07 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=1.59905e+07 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=1.59906e+07 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=1.59906e+07 beta=0.02
CLASS 1 MEAN 39.5182 STDDEV 22.8726 CLASS 2 MEAN 86.1827 STDDEV 11.9144 CLASS 3 MEAN 110.686 STDDEV 1.2016
Tanaka Iteration 1 bias field 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=1.59382e+07 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=1.60531e+07 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=1.60551e+07 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=1.60551e+07 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=1.60551e+07 beta=0.02
CLASS 1 MEAN 39.2031 STDDEV 22.3142 CLASS 2 MEAN 86.5207 STDDEV 11.9661 CLASS 3 MEAN 110.56 STDDEV 0.907204
Tanaka Iteration 2 bias field 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=1.59738e+07 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=1.60886e+07 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=1.60906e+07 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=1.60906e+07 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=1.60906e+07 beta=0.02
CLASS 1 MEAN 39.1693 STDDEV 22.3019 CLASS 2 MEAN 86.9174 STDDEV 12.1487 CLASS 3 MEAN 110.685 STDDEV 0.700111
Tanaka Iteration 3 bias field 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=1.60175e+07 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=1.61325e+07 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=1.61346e+07 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=1.61346e+07 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=1.61346e+07 beta=0.02
CLASS 1 MEAN 39.2376 STDDEV 22.3944 CLASS 2 MEAN 87.2518 STDDEV 12.318 CLASS 3 MEAN 110.801 STDDEV 0.472759
Tanaka Iteration 0 hyperparameter 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=1.6096e+07 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=1.62142e+07 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=1.62164e+07 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=1.62165e+07 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=1.62165e+07 beta=0.02
CLASS 1 MEAN 39.3526 STDDEV 22.5536 CLASS 2 MEAN 87.6346 STDDEV 12.5264 CLASS 3 MEAN 110.918 STDDEV 0.238533
BETA 0.1
Tanaka Iteration 1 hyperparameter 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.1
CLASS 1 MEAN 39.5463 STDDEV 22.7613 CLASS 2 MEAN 88.1374 STDDEV 12.8038 CLASS 3 MEAN 110.935 STDDEV nan
BETA 0.1
Tanaka Iteration 2 hyperparameter 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.1
CLASS 1 MEAN nan STDDEV nan CLASS 2 MEAN nan STDDEV nan CLASS 3 MEAN nan STDDEV nan
BETA 0.1
Tanaka Iteration 3 hyperparameter 4
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.1
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.1
CLASS 1 MEAN nan STDDEV nan CLASS 2 MEAN nan STDDEV nan CLASS 3 MEAN nan STDDEV nan
BETA 0.1
Starting Partial Volume Estimation
tissue 1 1.44581e+06
tissue 2 0
tissue 3 0
total tissue 1.44581e+06
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