Hello, I am having a problem with the mri_ca_normalize step in autorecon2. When I run autorecon2 (in the dev version: recon-all-nmr -subjid avm004 -autorecon2 -nosubcortseg -hemi lh), it gives me a message that norm.mgz is missing, and it seems that the files are not being created (either in the <subjid>/mri /norm folder or in norm.mgz format). I tried running mri_ca_normalize alone with the following command:
"mri_ca_normalize -mask avm004/mri/brain.mgz avm004/mri/nu.mgz ${FREESURFER_HOME}/average/RB40_talairach_2005-07-20.gca avm004/mri/transforms/talairach.xfm avm004/mri/norm.mgz"
and I get the following output, still with no norm.mgz or norm files:
reading atlas from '/usr/local/freesurfer/dev/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type reading transform from 'avm004/mri/transforms/talairach.xfm'... reading input volume from avm004/mri/nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=53.0 using (111, 120, 127) as brain centroid... mean wm in atlas = 110, using box (97,105,108) --> (125, 135,146) to find MRI wm before smoothing, mri peak at 184 after smoothing, mri peak at 184, scaling input intensities by 0.596 scaling channel 0 by 0.596172 using 269906 sample points... INFO: transform used GCApriorToSourceVoxelFloat: needs vox-to-vox transform
Is there some way to get the normalize step to run during autorecon2? Thanks for your help, Margo