On Aug 22, 2018, at 5:48 PM, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Can you send the terminal output and/or the log file?

On 08/22/2018 09:49 AM, Nada Naguib wrote:

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Hello, thank you for your response, yes My terminal is in the tcsh
shell so I’m not sure why it’s not working

Nada


On Aug 22, 2018, at 3:22 PM, Adam Martersteck <acmarter@gmail.com
<mailto:acmarter@gmail.com>> wrote:

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Are you sure you're terminal is setup in tcsh or csh? If you're using
bash instead, you want "export SUBJECTS_DIR=/project/bil/Nada"
Take a look at:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux to
see if you may have missed something.

On Wed, Aug 22, 2018 at 4:37 AM Nada Naguib <nadann@bu.edu
<mailto:nadann@bu.edu>> wrote:

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   Hello,

   I have been using bbregister in this format

   bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea
   register.lta

   NewT2out is the output of the free surfer processing on the T1
   image and dkti4d.nii is the template file I want to use for the
   registration.

   it has worked before but now there is a new error

   ERROR: cannot find NewT2out in
   /project/iconic/apps/freesurfer/5.3.0/install/subjects

   even though I have already ran the command:

   setenv SUBJECTS_DIRECTORY /project/bil/Nada


   This path is where both NewT2out and dkti4d.nii are located.

   I don’t understand what is going wrong

   Best
   Nada

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