Hi,
I'm not really sure what is happening here.
Can you upload one problematic dataset to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and send us the reference number. Hopefully
we can diagnose the problem then.
All the best,
Mark
On 25 Oct 2010, at 05:02, Zheng Hui wrote:
> Hi, can any FSL expert please kindly give some lights on my problem
> below. Thanks.
>
> ************************************
> 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.
>
>
> ************************************
> 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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