- Specifying a file basename as a variable
Write a script ("baserun") that echoes the basename (i.e. vol0001 for vol0001.nii.gz) of every file in a directory. You will need to use the command basename. Hint: basename vol0001.nii.gz .nii.gz will output vol0001
- Specifying multiple inputs
Modify one of the above script to use all of the user specified
arguments, rather than everything in the directory.
If you type
./baserun im2.nii.gz im3.nii.gz
you should get
im2
im3
- Multiple BET calls
Write a script that applies BET to all images in a directory.
Call the output images imagename_brain
Type
./baserun im2.nii.gz im3.nii.gz
and check that BET runs on these two images.
Look here for the cheat.
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