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...