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the full line after setting up the environment is 

recon-all -i /Users/ali?Arch_Raim/IM-0001-0001.dcm -s IM-0001 -all

On Wed, 10 Nov 2021 at 15:53, Tim Schäfer <ts+ml@rcmd.org> wrote:

        External Email - Use Caution       

Dear Alison,

Could you copy&paste the full command line that you are using to run recon-all?

Best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On 11/10/2021 4:48 PM Alison McDonnell <amcdonn8@tcd.ie> wrote:
>
> 
> External Email - Use Caution       
>
> when i run recon all it creates all the subfolders but they're empty. the
> only thing that is actually generated is orig.mgz and rawavg.mgz in the mri
> subfolder. i didn't get any errors when running recon all so was hoping
> someone could shed some light on this.
>
> Many thanks
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