Hi Diandra,

can you try running it with the current dev version and see if the problem goes away? Krish can get you a binary.

cheers Bruce On Thu, 15 Jul 2010, Diandra Lucia wrote:

Hi there,

We're processing some new 3T cases in FreeSurfer, and one case has been hanging just after it begins mri_ca_normalize:

#@# CA Normalize Wed Jul 14 17:16:05 EDT 2010 /home/pnlstaff/freesurfer/subjects/case01264/mri

mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz

using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/share/apps/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (62, 68, 28) --> (193, 185, 208) using (106, 107, 118) as brain centroid... mean wm in atlas = 107, using box (90,93,96) --> (122, 121,140) to find MRI wm before smoothing, mri peak at 164 after smoothing, mri peak at 163, scaling input intensities by 0.656 scaling channel 0 by 0.656442 using 244171 sample points... INFO: compute sample coordinates transform 1.058 0.020 -0.013 -10.456; -0.017 1.106 0.142 -38.892; 0.017 -0.123 0.973 10.525; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 70, 32) --> (190, 174, 202)

It doesn't give an error, it just hangs there, using 99.9% of the CPU. I checked the original T1 nifti and the brainmask and they look fine (we actually pre-skullstrip our T1s and copy them to create our brainmasks, and include -noskullstrip when we run autorecon-1). We're running these on freesurfer-Linux-rh9-stable-pub-v4.2.0.

We actually had a similar problem about a year ago, and you sent us the CentOS4 build of the mri_ca_normalize script which fixed it, but my colleague who downloaded it from you is on vacation for 2 weeks and then is leaving, and I think it's locked up in her login. So, if this turns out to be a good solution again, I'd need to download the file again.

Thanks for your help, Diandra