Hi Akio, The ribbon.mgz is created in autorecon3, just before the segstats step. So you will have to also run autorecon3. Since you have already run autorecon1 and 2 you will just need to run something like:
recon-all -autorecon3 -s <subjID> Sorry for the confusion. -Louis On Thu, 23 May 2013, Akio Yamamoto wrote: > Nick, > > I ran recon-all with -autorecon1 and -autorecon2 flags. > > Not exactly the same as the previous one, but I got another error in > mri_segstats. The recon-all.log file is also attached in this email. > > It seems likely that mri_segstats has been revised drastically in v5.2.0 or > later? > > Thanks in advance for your help. > > Akio > > ========== > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > cwd > cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv > mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg > --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol > --surf-ctx-vol --totalgray --euler --ctab > /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test > sysname Linux > hostname dhcp006 > machine x86_64 > user yamamoto > UseRobust 0 > atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) > mghRead(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/ribbon.mgz, > -1): could not open file > > > (2013/05/21 23:28), Nick Schmansky wrote: >> Akio, >> >> You should just run -autorecon2 instead of -subcortseg in order to get the >> subcortical segmentation. >> >> Nick >> >> >>> Hi Freesurfer experts, >>> >>> After installing v5.3.0 (CentOS 6 64bit), the command "recon-all -s test >>> -i sample-001.mgz -i sample-002.mgz -autorecon1" finished without error. >>> >>> Then, when I ran "recon-all -s test -subcortseg", I got the following >>> error: >>> >>> ========== >>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >>> cwd >>> cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv >>> mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg >>> --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz >>> --in-intensity-name norm --in-intensity-units MR --etiv --ctab >>> /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test >>> sysname Linux >>> hostname dhcp006 >>> machine x86_64 >>> user yamamoto >>> UseRobust 0 >>> atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) >>> MRISread(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.white): >>> could not open file >>> ========== >>> >>> I encountered this error in v5.2.0, and am still having the same error >>> in v5.3.0. >>> Is this a known issue? >>> >>> I attached the recon-all.log file. Any help is greatly appreciated. >>> >>> Best, >>> Akio >>> _______________________________________________ >>> 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. >> >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
