The names need to indicate image files, not directories (folders).
So if you do:
fslmaths L2 -add ...
then there needs to be a file L2.nii.gz (or L2.nii) in the current
directory. It just implicitly adds the .nii.gz (or .nii) to the name,
but otherwise acts like all other commands (e.g. ls) where you
need to tell it where the files are. If they are in the current
directory then nothing else is needed apart from the image name.
If they are in another directory then you have to specify that as
well, for example:
fslmaths diff_results/L2 -add ...
I hope this makes things clearer for you.
All the best,
On 2 Jun 2011, at 20:56, Jessica Perez wrote:
> Does it have to be a specific file that I direct fslmaths to or is directing it to an L2 folder okay?
> I direct the terminal to the folder that contains the L2 and L3 folder and then type in the command
> fslmaths L2 -add L3 -div 2 L23 .... so I don't know why it would not find the folder L2.
> Do I have to create a folder L23 in advance of typing the command for it to work?