Hi Doug,
I sent the log file, but had to shorten it because it was too large and couldn't be received on the mailing list. I've attached it here again. I can't send you the terminal window output as I have since closed the terminal window, but I could try re-running certain steps and sending you those outputs if that would help?
I ran 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). Then I added a few control points and added in white matter which was missing in between areas of white matter which were included in the wm mask. I then ran recon-all -s subject_no -make all -xopts-use. Then I ran recon-all -s subject_no -qcache which seemed to run ok, but exited with the error reading the curvature file. This error wasn't rectified by recon-all -s subject_no -make all as previous postings have found works.
Thank you.
Best wishes, Clare
________________________________________ From: Gibbard, Clare Sent: 25 July 2012 16:45 To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all
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 [fischl@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
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