Dear Franklin,
i have figured out my first problem and now I end up with almost the same error as you have.
Traceback (most recent call last):
File "/apps/prod/x86_64/fsl-5.0.10/bin/bianca", line 1033 in <module> p_main()
File "/apps/prod/x86_64/fsl-5.0.10/bin/bianca", line 1007 in p_main()
labels = labelvals[idvals]
IndexError: index 8933309 is out of bounds for axis 1 with size 0
My command:
bianca --singlefile=masterfile.txt --labelfeaturenum=4 --brainmaskfeaturenum=1 --querysubject=1 --trainingsnums=1,2,3 --featuresubset=1,2 --matfeaturenum=3 --trainingspts=2000 --nonlespts=1000 --selectpts=noborder -o sub2bianca
My masterfile:
subj01/20170322_123358t2FLAIR3dsagipatspules028a001.nii.gz subj01/T1_2_Flair.nii.gz subj01/T1_2_Flair.mat lesion.nii.gz
subj02/20170322_110016t2FLAIR3dsagipatspules028a001.nii.gz subj02/T1_2_Flair.nii.gz subj02/T1_2_Flair.mat lesion.nii.gz
subj03/20170306_150739t2FLAIR3dsagipatspules029a001.nii.gz subj03/T1_2_Flair.nii.gz subj03/T1_2_Flair.mat lesion.nii.gz
Background to Masterfile:
1 column is my FLAR image
2 column is my T1 registered on FLAIR
3 column is my transformation matrix
4 column is my binary roi with lesions, marked on space in FLAIR image
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