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
Hi Margo,
you should be using the talairach.lta file created by mri_em_register (not the talairach.xfm that you have in your command line).
cheers, Bruce
On Thu, 22 Dec 2005, Margo McKenna Benoit wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Margo McKenna Benoit