it might be - it's pretty much always the first thing to check. Note that leaving around some extra-cerebral tissue isn't a big deal. It's mostly only when the non-brain stuff connects to the white matter (incorrectly) and gets included in the surface that things break down.

On Mon, 2 Apr 2007, Derin Cobia wrote:

The talairach looks really bad, stretched beyond recognition and smeared, so I think I'll try renaming. What about the 1st subject I mentioned? Talairach bad with this one too? Thanks.

-Derin

...

Hi Derin,

the bad talairach is probably messing everything up. You can either correct it manually with tkregister2, or remove/rename the talairach.xfm and talairach.auto.xfm use recon-all with -notalairach so it won't be rebuilt. Nick: is there a flag to ignore the tal xform even if it's there? Something like -badtalairach?

cheers, Bruce

On Mon, 2 Apr 2007, Derin Cobia wrote:

...

Two questions for two different subjects during autorecon1:

1. The initial skull strip on this subject left too much extra-cerebral

material. Subsequent attempts at using the wsatlas or manual adjustment of the wsthresh have resulted in this error:

*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 1960516

 Find the largest 110-component...mriSegmentReallocateVoxels: could

not alloc 1048381 voxels for sno 8343 Cannot allocate memory done And identify it as the main brain basin...Segmentation fault Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Mon Apr 2 15:02:05 CDT 2007 #--------------------------------------------------------------

Are there too many voxels? I've looked, but couldn't find any information on how to fix this one.

2. This subject continues to fail with errors during intensity

normalization. Here is the output:

#-------------------------------------------- #@# Intensity Normalization Mon Apr 2 15:46:47 EDT 2007 /disk/conte_raid1/freesurfer/conte_mprage/021219_5734/mri

mri_normalize -g 1 nu.mgz T1.mgz

using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.830 -0.117 -0.004 -3.656; 0.116 0.833 -0.323 -26.577; 0.004 0.028 0.075 84.152; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Apr 2 15:46:49 EDT 2007 #---------------------------------------------

I've checked the talairach.xfm and it is bad. It seems I remember someone on the list saying that a -nold flag could fix this, but I couldn't find any info on the wiki about it. Any suggestions? Can I still salvage this subject?

Thanks for all of your help!

-Derin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

There is no -badtalairach flag or equivalent. Removing/renaming the talairach.xfm and talairach.auto.xfm files and using recon-all with - notalairach so it won't be rebuilt seems like it will work.

Bruce, maybe the -notalairach flag should rename the talairach.xfm and talairach.auto.xfm files if they exist?

On Mon, 2007-04-02 at 16:46 -0400, Bruce Fischl wrote:

Hi Derin,

the bad talairach is probably messing everything up. You can either correct it manually with tkregister2, or remove/rename the talairach.xfm and talairach.auto.xfm use recon-all with -notalairach so it won't be rebuilt. Nick: is there a flag to ignore the tal xform even if it's there? Something like -badtalairach?

cheers, Bruce

On Mon, 2 Apr 2007, Derin Cobia wrote:

...

Two questions for two different subjects during autorecon1:

1. The initial skull strip on this subject left too much extra-cerebral

material. Subsequent attempts at using the wsatlas or manual adjustment of the wsthresh have resulted in this error:

*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 1960516

 Find the largest 110-component...mriSegmentReallocateVoxels: could

not alloc 1048381 voxels for sno 8343 Cannot allocate memory done And identify it as the main brain basin...Segmentation fault Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Mon Apr 2 15:02:05 CDT 2007 #--------------------------------------------------------------

Are there too many voxels? I've looked, but couldn't find any information on how to fix this one.

2. This subject continues to fail with errors during intensity

normalization. Here is the output:

#-------------------------------------------- #@# Intensity Normalization Mon Apr 2 15:46:47 EDT 2007 /disk/conte_raid1/freesurfer/conte_mprage/021219_5734/mri

mri_normalize -g 1 nu.mgz T1.mgz

using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.830 -0.117 -0.004 -3.656; 0.116 0.833 -0.323 -26.577; 0.004 0.028 0.075 84.152; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Apr 2 15:46:49 EDT 2007 #---------------------------------------------

I've checked the talairach.xfm and it is bad. It seems I remember someone on the list saying that a -nold flag could fix this, but I couldn't find any info on the wiki about it. Any suggestions? Can I still salvage this subject?

Thanks for all of your help!

-Derin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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