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Before learning things systematically, here is a fairly simple script which is very powerful and useful for modifying for many different tasks.
#!/bin/sh
for filename in *.nii.gz ; do
fname=`$FSLDIR/bin/remove_ext ${filename}`
fslmaths ${fname} -s 2 ${fname}_smooth2
mv ${fname}.nii.gz ${fname}_smooth0.nii.gz
done
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What this does:
For each image (*.nii.gz) it smooths it to make a new one of the same name but ending in _smooth2 and also renames the unsmoothed image to end with _smooth0
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How this works:
- The variable
filename is used in a for loop to go through each name matching *.nii.gz
- The variable
fname is set to the filename with the ending (e.g. .nii.gz) removed.
Don't worry about how this works for now - the details will be explained later.
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${filename} and ${fname} are used to get the values (contents) of the variables
- fslmaths is used to do the smoothing.
- mv is used to do the renaming (notice that .nii.gz is needed here, but not for the fsl tools, as they work with or without the .nii.gz endings).
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