Hi Linlin,
Put all your images into one folder and name T1.nii.gz for example (with
your IDs appended, i.e. ID01_; ID02_. Then, within the terminal change
directory to that folder ('cd path_to_my_folder')
for f in *T1.nii.gz*; do bet $f ${f/T1/T1_brain} -v; done
You can check the functionality of the bet command by typing bet in the
terminal, it will list all options.
The for loop will not allow simultaneous brain extraction, but it will
go through all subjects sequentially. However, you can make different
batches of T1.nii.gz files in a few different folders (change the
directory within a new terminal window to that folder) and run the
command. This way you will run a couple of batches simultaneously.
Best wishes,
Barbara
On 01/05/2017 21:19, Linlin Gao wrote:
> Hi all,
>
> I have installed the FSL and have known how to remove the skull and extract the brain of an image by using the BET GUI, but I have no idea about how to batch remove the skull and extract the brains of many images simultaneously. Could you guys give me some help?
>
> Best wishes,
> Linlin Gao
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