make_initial_affine: 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/lib/cmtk/bin/make_initial_affine - from package: cmtk

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

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