Dear Mark and FSL experts,
I am trying to create ROI using fslmaths. My command lines are:
cd /usr/local/fsl/data/standard
fslmaths MNI152_T1_1mm.nii.gz -mul 0 -add 1 -roi 93 1 174 1 60 1 0 1 ROI2point -odt float
fslmaths ROI2point.nii.gz -kernel sphere 7 -fmean ROI2sphere -odt float
I am getting a very weird image (ROI2sphere.nii.gz) in which i can hardly see the created ROI, but rather it is surrounded by different patches of dark and white intensities. This problem disappeares at once if i am creating ROI of size 5 (or smaller).
I have seen a very similar post sometimes ago (i believe in 2008), but there was no a clear solution.
Is there anything i am doing wrong? I have reinstalled FSL just to be up to date (running on Mac, Yosemite, though, i do not think that the OS causes the problem).
I would greatly appreciate your suggestions/help/advise.
thank you
alla
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