Bruce et al,
Did you ever get to the bottom of Joakim's problem? I'm getting the same error. I checked the talairach and it looks fine. But for some reason mri_normalize can't find any peaks so T1.mgz comes out as all zeros.
I just uploaded the subject to your anon FTP server.: ex03.2.tgz
Thanks and let me know, -Adam
On Thu, Nov 2010, Bruce Fischl wrote:
Hi Joakim,
you need to visualize the talairach.xfm applied to the orig.mgz in either tkregister2 or tkmedit to see if it is ok. mri_normalize clearly failed, and this is usually because of a failure in the talairach. It could also be that the nu intensity correction failed, so make sure to look at the nu.mgz as well. Or if you rather you can send us the nu.mgz and we can see what happened. cheers Bruce
On Thu, 11 Nov 2010, Joakim Vinberg wrote:
Bruce,
I had quickly scanned the talairach.xfm, but I have to admit that I'm new to the process and wasn't sure what I was looking for. Here are the recon-all.log and talairach.xfm from this subject. Thank you for all the help!
oakimJ
-----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, November 10, 2010 7:09 PM To: Joakim Vinberg Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] another recon-all error
Did you check the talairach.xfm? Can you send us the recon-all.log file?
On Nov 10, 2010, at 9:35 PM, "Joakim Vinberg" jvinb...@omneuron.com wrote:
Sorry to add another!
I ran recon-all on a subject of mine, and have recon-all exit with the error below. Based on the message, I examined both T1 and nu.mgz. T1.mgz is in fact totally emptyÿÿdefinitely not enough values of 110. Is this due to a specific error that I might be able to bypass, or will adding in WM control points fix things?
Thanks in advance!
Joakim
//********************************************************
mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
Linux penguin 2.6.34.6-54.fc13.i686 #1 SMP Sun Sep 5 17:52:31 UTC 2010 i686 i686 i386 GNU/Linux
recon-all -s 0142 exited with ERRORS at Wed Nov 10 16:55:08 PST 2010
this is a problem that will be fixed in the upcoming 5.1 release (*hopefully* by the end of the year).
the workaround is to run mri_nu_correct.mni adding the -nofloat flag.
n.
On Wed, 2010-12-15 at 02:57 -0500, Thomas, Adam (NIH/NIMH) [E] wrote:
Bruce et al,
Did you ever get to the bottom of Joakim’s problem? I’m getting the same error. I checked the talairach and it looks fine. But for some reason mri_normalize can’t find any peaks so T1.mgz comes out as all zeros.
I just uploaded the subject to your anon FTP server.: ex03.2.tgz
Thanks and let me know,
-Adam
On Thu, Nov 2010, Bruce Fischl wrote:
Hi Joakim,
you need to visualize the talairach.xfm applied to the orig.mgz in either tkregister2 or tkmedit to see if it is ok. mri_normalize clearly failed, and this is usually because of a failure in the talairach. It could also be that the nu intensity correction failed, so make sure to look at the nu.mgz as well. Or if you rather you can send us the nu.mgz and we can see what happened.
cheers
Bruce
On Thu, 11 Nov 2010, Joakim Vinberg wrote:
Bruce,
I had quickly scanned the talairach.xfm, but I have to admit that I'm new to
the process and wasn't sure what I was looking for. Here are the recon-all.log
and talairach.xfm from this subject. Thank you for all the help!
oakimJ
-----Original Message-----
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 10, 2010 7:09 PM
To: Joakim Vinberg
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] another recon-all error
Did you check the talairach.xfm? Can you send us the recon-all.log file?
On Nov 10, 2010, at 9:35 PM, "Joakim Vinberg" jvinb...@omneuron.com wrote:
Sorry to add another!
I ran recon-all on a subject of mine, and have recon-all exit with the error
below. Based on the message, I examined both T1 and nu.mgz. T1.mgz is in fact
totally emptyÿÿdefinitely not enough values of 110. Is this due to a specific
error that I might be able to bypass, or will adding in WM control points fix
things?
Thanks in advance!
Joakim
//********************************************************
mri_watershed -T1 -brain_atlas
/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
Linux penguin 2.6.34.6-54.fc13.i686 #1 SMP Sun Sep 5 17:52:31 UTC 2010 i686
i686 i386 GNU/Linux
recon-all -s 0142 exited with ERRORS at Wed Nov 10 16:55:08 PST 2010
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Thomas, Adam (NIH/NIMH) [E]