Hi Mark

have you looked at the atlas? You can view it directly with freeview to see what the actual means are. What command line did you use to build it? Bruce On Mon, 21 Apr 2014, Mark Plantz wrote:

Hi freesurfers,   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