Hi Miklos, did you run all the steps that go before autorecon2? doug
On 04/16/2013 12:23 PM, Miklos Argyelan wrote: > Hi, > > I have recently installed Freesurfer on a new computer, and downloaded > the latest version of Freesurfer (centos 64 bit) and when ran: > > recon-all -subject test001 -autorecon2 > > I got the following error message: > > $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/ASegStatsLUT.txt --subject test001 > sysname Linux > hostname mikbox > machine x86_64 > user amiklos > UseRobust 0 > atlas_icv (eTIV) = 1444225 mm^3 (det: 1.348893 ) > *mghRead(/home/amiklos/nethome/work/METHODS/FS/subjects/test001/mri/ribbon.mgz, > > -1): could not open file* > > I am not sure but the bug seems that autorecon2 tries to run SegStats > too early (supposed to be in autorecon3). > > Maybe this is the error in recon-all: > case "-autorecon2": > set DoGCAReg = 1; > set DoCARegInv = 1; > set DoRemoveNeck = 1; > set DoSkullLTA = 1; > set DoCANormalize = 1; > set DoCAReg = 1; > set DoCALabel = 1; > *set DoSegStats = 1;* > set DoNormalization2 = 1; > set DoMaskBFS = 1; > set DoSegmentation = 1; > set DoFill = 1; > set DoTessellate = 1; > set DoSmooth1 = 1; > set DoInflate1 = 1; > set DoQSphere = 1; > set DoFix = 1; > set DoSmooth2 = 1; > set DoInflate2 = 1; > set DoWhiteSurfs = 1; > set DoCurvStats = 1; > breaksw > > Could some expert verify please that this is indeed the problem and I > can change the 1 to zero, or am I completely off? > > Miklos > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
