Dear experts,
even though there was a discussion here on how to creat spherical roi's
from the shell using fslmaths, these commands don't seem to work for me.
I tried the following to generate a point mask first:
fslmaths MNI_T1_2mm_brain_mask.nii.gz -roi 17 1 5 1 -7 1 point_mask -odt
float
The resulting mask was empty (zero). I also tried without -odt float, the
result being the same. Next I manually created a point mask in fslview at
MNI coordinates 17 5 -7. Then I issued the command
fslmaths point_mask.nii.gz -kernel sphere 5 -fmean -bin sphere_5mm_mask
This worked out, however, if I used a radius larger than 5 (6 to 9), the
resulting mask was an odd looking arrangement of blobs of intensity 1
interspersed with blobs of intensity zero - not only within the roi but
distributed all over the brain. Kind of weird. Does anyone have an idea
what went wrong here? In particular, why would things work fine with 5 mm
radius but not with 6 or 7 mm?
Thank you very much in advance,
greetings,
Gerhard
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