Hi Michal - Are you running the freesurfer setup script?

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration

Also, in your config file:
    - You're missing a "\" at the end of the line with the first nifti file
    - bvalfile is for defining a single b-value table, not multiple ones

Best,
a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of michal heker [michalheker@gmail.com]
Sent: Tuesday, December 27, 2016 7:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] flirt: command not found

Hello freesurfer developers,

I am trying to use TRACULA reconstruction with Virtual Box on my data (I have my own nii files). I have followed all the stages in the freesurfer tutorial. 

I get the following problem:

INFO: SUBJECTS_DIR is /media/sf_share/diffusion_recons
INFO: Diffusion root is media/sf_share/diffusion_ourbrains
Actual FREESURFER_HOME /usr/local/freesurfer
flirt: Command not found.
dcmlist: Subscript out of range.

What am i doing wrong?

find attached is a copy of my dmrirc file

Thanks for your help,
Michal