Error in executing command dwi2response: OSError: [Errno 2] No such file or directory

I am getting error in executing dwi2response command. The command and error is shown below.
Getting no clue why it is giving me error “No such file or directory”.
I have DWI.mif file present in my Mrtrix3 folder.
Is it something related to msmt_5tt?
I try to use scripts/src/dwi2response/msmt_5tt , but got error Error: invalid choice: ‘scripts/src/dwi2response/msmt_5tt’ (choose from ‘manual’, ‘tournier’, ‘tax’, ‘fa’, ‘msmt_5tt’)

.. koushik@koushik-DQ67SW:~/mrtrix3$ scripts/dwi2response msmt_5tt dwi.mif 5TT.mif RF_GM.txt RF_WM.txt RF_CSF.txt -voxels RF_voxels.mif dwi2response: dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Plea se consult the help page (-help option) for more information. dwi2response: dwi2response: Generated temporary directory: /tmp/dwi2response-tmp-EX8ZJO/ Command: mrconvert /home/koushik/mrtrix3/5TT.mif /tmp/dwi2response-tmp-EX8ZJO/5t t.mif Command: mrconvert /home/koushik/mrtrix3/dwi.mif /tmp/dwi2response-tmp-EX8ZJO/dw i.mif -stride 0,0,0,1 dwi2response: Changing to temporary directory (/tmp/dwi2response-tmp-EX8ZJO/) Traceback (most recent call last): File "scripts/dwi2response", line 110, in <module> size = getHeaderInfo('dwi.mif', 'size').split() File "/home/koushik/mrtrix3/scripts/lib/", line 7, in getHeade rInfo proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None) File "/usr/lib/python2.7/", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

Quick response please.


Sound like you haven’t set your PATH, as described in the docs? The scripts need to invoke MRtrix3 commands. If they’re not in the PATH, it won’t be able to find them.

To check whether MRtrix3 is in the PATH:

$ echo $PATH

To check whether mrinfo (which is the command needed for the step above) in in your PATH, and which version is being invoked:

$ which mrinfo

Thanks for the help. I set the PATH and it is executing correctly. I missed the step during installation.