nifti_tool: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/nifti_tool - from package: nifti-bin

You may install the required package with command apt-get install {package}

Error in other languages:
nifti_tool: bevel nie gevind nie
nifti_tool: comandă negăsită
nifti_tool: comando não encontrado
nifti_tool: commande introuvable
nifti_tool: command not found
nifti_tool: käsku ei ole
nifti_tool: không tìm thấy lệnh
nifti_tool: komanda nerasta
nifti_tool: Kommando nicht gefunden.
nifti_tool: kommandot finns inte
nifti_tool: komut yok
nifti_tool: nie znaleziono polecenia
nifti_tool: níor aimsíodh an t-ordú
nifti_tool: no se encontró la orden
nifti_tool: no s'ha trobat l'ordre
nifti_tool: opdracht niet gevonden
nifti_tool: parancs nem található
nifti_tool: perintah tidak ditemukan
nifti_tool: príkaz nenájdený
nifti_tool: příkaz nenalezen
nifti_tool: команда не найдена
nifti_tool: командата не е открита
nifti_tool: 命令找不到
nifti_tool: コマンドが見つかりません