Re-index all folders

Finished the setup of filerun and seems like everything goes well,i've transfered the archive to the new server but due to size of the archive i had to do it via copy from usb disk backups(approx 4 TB of folders and files.). 

As far as i know filerun search is working well if you transfer files/folders through filerun's interface, because of my transfer way search is not working now.

Is it possible to re-index all folders and files manually? 

As far as i understand from documents it is possible through running "index_filenames.php" from terminal, but just i want to be sure before run it.