Hi Yongxia, You need to add the matlab binary into your path. doug

On 05/22/2013 09:26 PM, Yongxia Zhou wrote:

Hi, I have a question running fsfast in my Mac, The mkcontrast command gave the error of can not launch matlab. Could you please let me know how to solve this problem. Thank you very much

Yongxia

On Wednesday, May 22, 2013, wrote:

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   1. recon-all error (Yizhou Ma)
   2. Re: Still confused by group analysis.. (Tudor Popescu)
   3. Re: ERROR in long_mris_slope (Martin Reuter)
   4. Re: ERROR in long_mris_slope (Martin Reuter)
   5. temporal lobe left out in pial surface - edits on
      brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
   6. Re: temporal lobe left out in pial surface - edits on
      brainmask.mgz or brain.finalsurfs.mgz? (Chris Watson)
   7. Re: temporal lobe left out in pial surface - edits on
      brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
   8. Re: temporal lobe left out in pial surface - edits on
      brainmask.mgz or brain.finalsurfs.mgz? (Bruce Fischl)
   9. Re: temporal lobe left out in pial surface - edits on
      brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
  10. Re: temporal lobe left out in pial surface - edits on
      brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
  11. Re: ERROR: recon-all -subcortseg (Akio Yamamoto)


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Message: 1
Date: Wed, 22 May 2013 13:19:35 -0400
From: Yizhou Ma <ym850@nyu.edu>
Subject: [Freesurfer] recon-all error
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:

<CAHqJiV6t-fKQRWcfFg8r5O9gJrtZsTe+ZgKU0qVD2J7aoNSVHw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear FS experts,

I have a recon-all error regarding one of my subjects. The scan
suffers
from weakened signals at the lower part of the brain. Skullstrip
stripped
most of the cerebellum at first, and we fixed it manually. After
running
recon-all for the first time, large portions of the temporal lobes
were
left out of the brain. Knowing that this may not be the correct
way, we
still tried to fixed that by adding lots of control points. The
second run
of recon-all, then, came back with the following error message:"

Loading source data
Reading curvature file
/space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness
ERROR: number of vertices in
/space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness
does not match surface (192226,134773)
ERROR: reading curvature file
Linux mmil-compute-1-11.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2
22:01:43
EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub4422b exited with ERRORS at Mon May 20
"

Any ideas for why it is, or how we can fix the problem at the temporal
lobes, will be really appreciated.

Thanks,
Cherry