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: >> >> #-------------------------------------------- >> [EMAIL PROTECTED] 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 >> >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
