Hi Bruce,
Thank you for your quick reply. I installed v5.1.0 from the website and that name is what comes up when I open a terminal window. However, I tried typing recon-all -version and got $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $. So I'm not sure if that means the version is different from what I thought.
I tried to upload 3 directories to the FTP in /transfer/incoming/claregibbard.tar. subject_1010_orig is the subject before adding control points. subject_1010_cpleft is after I added control points to the left temporal lobe. subject_1010_cpleftandright is when I tried adding control points to both the left and right temporal lobe. However, I can't tell if they have uploaded or not (it was taking a long time, but when I aborted the upload it said File receive OK). If you need me to, I can try sending you fewer files.
I hope that helps. Let me know if you need any more information.
Best wishes, Clare
________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 10 January 2012 13:40 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe cut off
Hi Claire,
hmmm, that is odd. What version are you running? If you upload the subject before and after we'll take a look Bruce On Tue, 10 Jan 2012, Gibbard, Clare wrote:
Hi,
I ran recon-all -all -subjid subjectx on around 40 scans. The registrations and skull strips look fine. However, the white matter and pial surface segmentations miss out the left anterior temporal lobe in most subjects. I tried adding in control points to the left temporal lobe and running recon-all -autorecon2-cp -autorecon3 -subjid subjectx. This helped to fill in the missing areas, but new parts of the right temporal lobe were cut out. I then tried adding in control points to both the left and right temporal lobes, but again new regions of the left temporal lobe were cut out. I think it must be an intensity issue, but I can't see how to fix it. Are you able to give me a work flow to sort this?
Here are some screenshots:
[moz-screenshot.png] [moz-screenshot-1.png] Before control points added:
[IMAGE]
After control points added to left and right temporal lobes:
[IMAGE]
Thank you.
Best wishes, Clare Gibbard
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