Subject 20 is definitely out of synch, but the "make all" feature is not catching it. Try re-running this subject with -autorecon3
doug On 07/25/2012 11:45 AM, Gibbard, Clare wrote: > Hi Bruce, > > Thanks, I've attached the end of the recon-all.log file for one of the > subjects (the whole thing was too large). This is what I get when I run > recon-all -version: > $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ > > When I try to run recon-all -s subject_no -make all I don't think anything > comes up in the log. I get this in the terminal window: > clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Subject 'subject_20': make all > make: Nothing to be done for `all'. > clare@clare-OptiPlex-990:~/subjects$ > > Let me know if you need anything else. Thank you. > > Best wishes, > Clare > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: 25 July 2012 14:44 > To: Gibbard, Clare > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Recon-all -qcache curvature error& recon-all make > -all > > Hi Clare > > can you send us the screen output and also what version you are running? > > thanks > Bruce > On > Wed, 25 Jul 2012, Gibbard, Clare wrote: > >> Hello, >> >> I have run several scans using recon-all -all -subjid subject_no -expert >> expert.opts where my expert.opts file changes the parameters for the >> mri_normalize step (this works well in my scans). I then had to edit a few >> of the scans by adding in more white matter and a few control points. I >> re-ran them to incorporate the edits using recon-all -s subject_no -make all >> -xopts-use. This worked well. >> >> I then ran recon-all -s subject_no -qcache ready for doing a group >> analysis. I got an error reading the curvature file in those subjects I had >> edited. I can see from the mailing list that others have had this error >> previously and ran recon-all -s subject_no -make all to fix it. I tried >> this, but I got a message saying that there was nothing to be done for all. >> >> Are you able to advise me on what I can try now? Do I need to go back a >> step? >> >> Thank you very much, >> Clare >> >> > > 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 -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
