I am running into an error where the white matter and gray matter means of my atlas are automatically setting to 0 during the #@# CA Normalize pathway. I copied a code segment below to help explain better. Has anyone else run into this problem? Is there a way to manually change these averages?
#@# CA Normalize Mon Apr 14 17:03:07 CDT 2014
/Applications/freesurfer/subjects/CMH-11780/mri
\n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/atlas2.gca transforms/talairach.lta norm.mgz \n
writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/Applications/freesurfer/average/atlas2.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 0 --> 0
resetting gm mean[0]: 0 --> 0
input volume #1 is the most T1-like
using real data threshold=27.0
skull bounding box = (64, 79, 51) --> (194, 166, 204)
using (107, 108, 128) as brain centroid...
mean wm in atlas = 0, using box (91,97,109) --> (122, 118,146) to find MRI wm
before smoothing, mri peak at 110
after smoothing, mri peak at 111, scaling input intensities by 0.000
scaling channel 0 by 0
using 136509 sample points...
INFO: compute sample coordinates 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: transform used
Thank you for the help.
- MP