nii2mnc: 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/nii2mnc - from package: minc-tools

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

Error in other languages:
nii2mnc: bevel nie gevind nie
nii2mnc: comandă negăsită
nii2mnc: comando não encontrado
nii2mnc: commande introuvable
nii2mnc: command not found
nii2mnc: käsku ei ole
nii2mnc: không tìm thấy lệnh
nii2mnc: komanda nerasta
nii2mnc: Kommando nicht gefunden.
nii2mnc: kommandot finns inte
nii2mnc: komut yok
nii2mnc: nie znaleziono polecenia
nii2mnc: níor aimsíodh an t-ordú
nii2mnc: no se encontró la orden
nii2mnc: no s'ha trobat l'ordre
nii2mnc: opdracht niet gevonden
nii2mnc: parancs nem található
nii2mnc: perintah tidak ditemukan
nii2mnc: príkaz nenájdený
nii2mnc: příkaz nenalezen
nii2mnc: команда не найдена
nii2mnc: командата не е открита
nii2mnc: 命令找不到
nii2mnc: コマンドが見つかりません