Re: [Freesurfer] -qcache / fsaverage / number of vertices errors

2014-01-24 Thread Bruce Fischl
yes, although why -make all didn't fix things is a mystery to me. On Fri, 24 Jan 2014, Mihaela Stefan wrote: Yes, -make all ran for about 7 hours and it exited without errors. How should I fix this?  What about -qcache after  recon-all -autorecon2-cp -autorecon3 -subjid ? Can I use that if it

Re: [Freesurfer] -qcache / fsaverage / number of vertices errors

2014-01-24 Thread Mihaela Stefan
Yes, -make all ran for about 7 hours and it exited without errors. How should I fix this? What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid ? Can I use that if it exited without errors? Can I assume that the subject has all the correct files and continue my analysis? Thanks!

Re: [Freesurfer] -qcache / fsaverage / number of vertices errors

2014-01-24 Thread Bruce Fischl
it's possible that the timestamps on your system are wrong I guess. Did -make all run anything? On Fri, 24 Jan 2014, Mihaela Stefan wrote: Hi Bruce, I used that command and I got the same errors when I ran -qcache again. I also found that my colleague, who did the edits, used the same command

Re: [Freesurfer] -qcache / fsaverage / number of vertices errors

2014-01-24 Thread Mihaela Stefan
Hi Bruce, I used that command and I got the same errors when I ran -qcache again. I also found that my colleague, who did the edits, used the same command after she manually edited the recons. I re-ran the subject with the following command recon-all -autorecon2-cp -autorecon3 -subjid and, when i

Re: [Freesurfer] -qcache / fsaverage / number of vertices errors

2014-01-23 Thread Bruce Fischl
Hi Mihaela usually that means the subject was partially but not completely rerun. You can try using recon-all -s -make all and see if it fixes it cheers Bruce On Thu, 23 Jan 2014, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a group analysis with Qdec following thistutorial