Thanks, Nick! I'll plan to try to series you suggested then. Fingers crossed, Mia
> On May 17, 2015, at 3:03 PM, "Nick Schmansky, MGH" > <ni...@nmr.mgh.harvard.edu> wrote: > > Mia, > > Hi, I took a quick look at your BI22_SurferOutput/mri/orig/001.mgz and > the problem appears to be with this input. The orientation is wrong, > and it doesnt quite look like an mprage or equivalent. Unfortunately, > after looking through your dicom series, it doesnt look like any of them > are ideal for freesurfer. the best option though is 8964, although its > 0.5x0.5x2mm. its a T1 and the orientation is correct, so it might > recon. > > Nick > > > > >> On Sun, 2015-05-17 at 16:33 +0000, Borzello, Mia wrote: >> Hi Freesurfers, >> >> >> Hope you're doing well! I tried creating a reconstruction yesterday >> but got an error. >> >> >> 1)BI22 >> 2)recon-all -autorecon1 -autorecon2 -autorecon3 -subject >> BI22_SurferOutput >> -i >> /autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/8961/8968/896583 >> 3) >> >> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0.0049, pval=0.0000 < threshold=0.0050) >> Manual Talairach alignment may be necessary, or >> include the -notal-check flag to skip this test, >> making sure the -notal-check flag follows -all >> or -autorecon1 in the command string. >> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >> UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> >> recon-all -s BI22_SurferOutput exited with ERRORS at Sat May 16 >> 19:44:42 EDT 2015 >> >> >> Let me know if including the recon-all.log would be helpful. >> >> >> Thanks so much, >> Mia >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
