Hi Michal - Are you running the freesurfer setup script?

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

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