mk_nifti_hdr: command not found

Have You tried accessing the binary with the full path?

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

[root@server ~]# echo $PATH

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/mk_nifti_hdr - from package: cmtk

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