Dear Mark and Matt,
thank you very much for your reply. The command I initially used was
fslmaths /daten/share/opt/fsl/fsl-4.0.1/data/ standard/
MNI152_T1_2mm_brain_mask.nii.gz -roi 17 1 5 1 -7 1 point_mask -odt float
The resulting mask was zero:
fslstats point_mask -R
0.0000 0.0000
I also tried the command you just recommended:
fslmaths /daten/share/opt/fsl/fsl-4.0.1/data/standard/
MNI152_T1_2mm_brain_mask.nii.gz -mul 0 -add 1 -roi 17 1 5 1 -7 1
point_mask -odt float
However, the result was the same as above.
So, I manually drew a point mask in fslview, to which I then applied the
following command:
fslmaths point_mask.nii.gz -kernel sphere 9 -fmean bin sphere9mm -odt float
The result was:
fslstats sphere9mm -R
0.0000 1.0000
however, what I obtained was the weird arrangement of blobs of ones and
zeros throughout the brain.
Also, the filesize is by far larger than with the 5 mm sphere (for a 5 mm
sphere, the file size was 28 K, whereas for a 6 mm spere it exceeded 1 MB).
Next, I tried the command as you suggested:
fslmaths point_mask.nii.gz -kernel sphere 9 -fmean sphere9mm -odt float
fslstats sphere9mm -R
0.000000 0.000326
The mask now has 0.00033 intensity while it is still surrounded by blobs
of varying intensity.
This is what happened to me here. I am looking forward to your opinion on
this,
Thank you and best regards,
Gerhard
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