I am running the fsl_anat script to allow bias field correction and better brain extraction on t1 anatomicals using the following command:
fsl_anat --nosubcortseg --clobber -i t1.nii.gz
A limited number of scans (6 out of 51) despite all being collected on the same scanner comes up with the following error message:
Wed Feb 11 19:34:56 GMT 2015
Reorienting to standard orientation
Wed Feb 11 19:35:13 GMT 2015
Automatically cropping the image
Wed Feb 11 19:35:22 GMT 2015
Estimating and removing field (stage 1 - large-scale fields)
Wed Feb 11 19:35:55 GMT 2015
Estimating and removing bias field (stage 2 - detailed fields)
Starting Single Image Segmentation
T1-weighted image
Imagesize : 150 x 256 x 181
Pixelsize : 1.2 x 0.9375 x 0.9375
1 10.2409
2 10.2436
3 10.2457
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
MeaNsK variance nan
MeaNsK variance nan
MeaNsK variance nan
Tanaka Iteration 0 bias field 5
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.02
CLASS 1 MEAN nan STDDEV nan CLASS 2 MEAN nan STDDEV nan CLASS 3 MEAN nan STDDEV nan
Tanaka Iteration 1 bias field 5
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.02
CLASS 1 MEAN nan STDDEV nan CLASS 2 MEAN nan STDDEV nan CLASS 3 MEAN nan STDDEV nan
Tanaka Iteration 2 bias field 5
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.02
CLASS 1 MEAN nan STDDEV nan CLASS 2 MEAN nan STDDEV nan CLASS 3 MEAN nan STDDEV nan
Tanaka Iteration 3 bias field 5
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.02
CLASS 1 MEAN nan STDDEV nan CLASS 2 MEAN nan STDDEV nan CLASS 3 MEAN nan STDDEV nan
Tanaka Iteration 4 bias field 5
Tanaka-inner-loop-iteration=0 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=1 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=2 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=3 MRFWeightsTotal=0 beta=0.02
Tanaka-inner-loop-iteration=4 MRFWeightsTotal=0 beta=0.02
CLASS 1 MEAN nan STDDEV nan CLASS 2 MEAN nan STDDEV nan CLASS 3 MEAN nan STDDEV nan
tissue 1 0
tissue 2 0
tissue 3 0
total tissue 0
Starting Single Image Segmentation
T1-weighted image
Imagesize : 150 x 256 x 181
Pixelsize : 1.2 x 0.9375 x 0.9375
1 0
2 0
3 0
Exception: Not enough classes detected to init KMeans
Any ideas?
Thanks
Tony
Dr. Tony Goldstone MA MRCP PhD
Centre for Neuropsychopharmacology and Computational, Cognitive and Clinical Neuroimaging Laboratory
Division of Brain Sciences, Imperial College London
3rd Floor Burlington Danes Building
Imperial College London
Hammersmith Hospital
Du Cane Road
London W12 0NN
[log in to unmask]
|