Hi Jeff,

I've seen this happen before with the N3 stuff where it reduces the image intensities so much that you start losing dynamic range. Not sure what causes it, but you could cp orig.mgz to nu.mgz and run from there forward.

cheers, Bruce On Wed, 24 Sep 2008, Jeff Sadino wrote:

Hello all,

I am receiving an error when trying to run autorecon1. When trying to step through it manually step-by-step, everything is fine up to -nuintensitycor. After running that command and looking at nu.mgz in tkmedit, the picture starts to fade out pretty bad above 120 intensity. When I lower the intensity down to about 30, I can see the picture just fine. Next, I skip -talairach (even though and run -normalization. But it exits with an error:

[FSuser@cluster mri]$ recon-all -s 070046_S01 -normalization INFO: SUBJECTS_DIR is /data Actual FREESURFER_HOME /apps/freesurfer -rw-rw-r-- 1 FSuser FSuser 90352 Sep 24 16:10 /data/070046_S01/scripts/recon-all.log Linux cluster.mrilab.net 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Intensity Normalization Wed Sep 24 16:15:19 HST 2008 /data/070046_S01/mri

mri_normalize -g 1 nu.mgz T1.mgz

using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 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 cluster.mrilab.net 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Sep 24 16:15:21 HST 2008

Also, I have some of the -talairach files from a previous run:

[FSuser@cluster mri]$ ls transforms/ bak talairach.auto.xfm talairach.log talairach.xfm

Any ideas? Thank you. Jeff _________________________________________________________________ Get more out of the Web. Learn 10 hidden secrets of Windows Live. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!55... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer