Re: [Freesurfer] Recon-all -i ... command does not create all 10 folders

You can try executing it with the -dontrun option doug Juergen Haenggi wrote: Dear Freesurfer users we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed w

Re: [Freesurfer] Recon-all -i ... command does not create all 10 folders

Hi Juergen, you can use -noaseg and only do one hemisphere (-hemi lh) which should make it quite a bit faster, but of course it won't work as well without the aseg. Did you check the recon-all.log to see if it had errors making directories? Although it should have aborted then. cheers, Bruce

[Freesurfer] Recon-all -i ... command does not create all 10 folders

Dear Freesurfer users we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed when trying to write lh.aparc.annot, because there is no folder called label. We then