Hi Matt

can you try running in two separate steps? First -all then when it completes run recon-all again with -FLAIRpial?

On Thu, 28 Sep 2017, Hibert, Matthew Louis wrote:

Hi All, Any thoughts on the error we encountered? I attached the log again for convenience.

Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu] Sent: Monday, July 17, 2017 4:40 PM To: Freesurfer support list Cc: Gholipour, Taha,M.D. Subject: Re: [Freesurfer] dev -FLAIRpial bug?

Sorry, forgot to attach the log.

Matt ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu] Sent: Monday, July 17, 2017 4:39 PM To: Freesurfer support list Cc: Gholipour, Taha,M.D. Subject: [Freesurfer] dev -FLAIRpial bug?

Hi FS Devs, We're running some reconstructions of 7T MPRAGEs with the -FLAIRpial flag turned on using the Martinos install of the dev version. Recently we encountered the error in the attached recon-all log in which it appears that recon-all is trying to use the aseg.mgz before it has been created. According to the dev table online, the mris_make_surfaces command as part of the -FLAIRpial processing should use aseg.presurf.mgz, but it crashes with an error that it was unable to open aseg.mgz.

Thanks, Matt