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Please search the forum for similar questions that have already been answered before posting a new question. Without knowing what the format of other filenames in your directories, you could use a find command searching exactly for filenames ending with those two strings in the file hierarchy rooted in the current working directory:

Code:

find . -name '*eddy_corrected.nii.gz' -o -name '*eddy_corrected_brain_mask.nii.gz'

If there aren't any other names containing eddy_corrected that end with nii.gz you could use the simpler:

Code:

find . -name '*eddy_corrected*nii.gz'

The terminal application running in your window manager emulates a terminal from days of yore. The terminal application just emulates hardware, it doesn't run commands, it doesn't create file, it doesn't do anything except emulate a terminal device. When you start (or your system starts) the terminal application, you specify a program to run in that terminal window. Usually the program that you run in a terminal window will be a command interpreter such as bash, csh, ksh, or zsh. These command interpreters are known as shells. The commands recognized by different shells varies. All of the examples I'm suggesting in this post will work with bash, ksh, and zsh; some, but not all, will work in csh.
Adding > filename to the end of either of the above commands will redirect the output from those commands to the file named filename (creating the file if it does not exist, and overwriting its previous contents if it did exist). Using >> filename will append the output of those commands will create the file if it did not exist and append the output to the end of the file if it did exist.
You could try something like:

Code:

find . -name '*DTISiemensTCless*.bvec' -o -name '*DTISiemensTCless*.bval' |
while read -r path
do	dir="${path%/*}"
	file="${path##*/}"
	subjectnumber="${file%%DTI*}"
	ext="${file##*.}"
	echo mv "$path" "$dir/${subjectnumber}DTI.$ext"
done

(this assumes that you want to preserve the .bvec or .bval at the ends of the pathnames) and if the output looks like it correctly supplies the proper arguments to rename files the way you want them to be, remove the echo shown in red and rerun the command to actually rename the files. If you want to the new names of all of the files to have the extension .bvec, change the two lines:

Code:

	ext="${file##*.}"
	echo mv "$path" "$dir/${subjectnumber}DTI.$ext"

to be just:

Code:

	echo mv "$path" "$dir/${subjectnumber}DTI.bvec"

This is a perfectly reasonable forum for this topic.