Hi all,
I have been trying to process an image, and the reconstruction has been consistently freezing at the same spot. This brain failed the tailarach transform, but I checked it and it looked fine, so I used the -notal-check flag. I have had this happen with several other brains, and there was no problem using this flag until now. I have tried it on 2 different computers where we have FreeSurfer, and it still freezes at the exact same place. I left it overnight to be sure it was really frozen, and the next morning the reconstruction script had not progressed. There is no error message. The place where it freezes is mri_ca_normalize, and I have pasted the script below:
#@# CA Normalize Thu Jul 2 18:31:14 EDT 2009 /home/dwm2003/NPH/FS/NPH3/mri
mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/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 '/usr/local/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=17.0 skull bounding box = (56, 38, 29) --> (205, 184, 175) using (106, 87, 102) as brain centroid... mean wm in atlas = 107, using box (88,69,84) --> (124, 104,119) to find MRI wm before smoothing, mri peak at 88 after smoothing, mri peak at 87, scaling input intensities by 1.230 scaling channel 0 by 1.22989 using 244171 sample points... INFO: compute sample coordinates transform 0.926 -0.053 0.111 2.200; 0.005 0.987 0.482 -32.821; -0.126 -0.444 0.940 78.347; 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 (124, 43, 29) --> (200, 162, 179) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 110.0 115 of 354 (32.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (58, 45, 28) --> (131, 156, 177)
This is always where the script stops when the process seems to freeze. (I have tried 3 times with the same result). Any ideas?
Thanks, Dana
Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu