Hi,
I recently ran the following set of commands on a series of EPI images
(run1, run2...run6) in order to remove some noise and other artifacts
outside of the brain (e.g., eyes):
================
#!/bin/bash
mkdir run1
mkdir run2
mkdir run3
mkdir run4
mkdir run5
mkdir run6
mv s001.nii run1/
mv s002.nii run2/
mv s003.nii run3/
mv s004.nii run4/
mv s005.nii run5/
mv s006.nii run6/
for f in run*; do
cd $f
fslsplit *nii
cd ..
done
for f in run*; do
cd $f
fslsplit *nii
cd ..
done
for f in run*; do
cd $f
for ff in vol*; do
bet2 $ff b${ff}
done
cd ..
done
fslmerge -t imageAfter bvol*
=================
Is this an appropriate use of bet2, or is it essentially doing the same
thing as a mask at a later preprocessing stage? One reservation I have is
that the process appeared to artificially inflate the image intensity. Any
input is appreciated.
Thank you,
-Andrew
|