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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis > [mhib...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis > [mhib...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
