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