Summary logfile for mri_cvs_register
Wed 14 Dec 20:40:38 GMT 2016
--template SynthF --mov SynthN --outdir CVS
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
stefano-Q170M-C
Linux stefano-Q170M-C 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
asegfname aseg
Initializing the mri_cvs_register run
Using m3z type morph files.
Ready for spherical registration (CVS: Step 1)
mris_register -1 -dist 1.0 -inflated /usr/local/freesurfer/subjects/SynthN/surf/lh.sphere /usr/local/freesurfer/subjects/SynthF/surf/lh.sphere /usr/local/freesurfer/subjects/SynthN/surf/lh.cvs.toSynthF.sphere.reg
mris_register -1 -dist 1.0 -inflated /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere /usr/local/freesurfer/subjects/SynthF/surf/rh.sphere /usr/local/freesurfer/subjects/SynthN/surf/rh.cvs.toSynthF.sphere.reg
mris_resample --atlas_reg /usr/local/freesurfer/subjects/SynthF/surf/lh.sphere --annot_in /usr/local/freesurfer/subjects/SynthN/label/lh.aparc.annot --annot_out CVS/lh.resample.aparc.annot --subject_surf /usr/local/freesurfer/subjects/SynthN/surf/lh.white --subject_reg /usr/local/freesurfer/subjects/SynthN/surf/lh.cvs.toSynthF.sphere.reg --out CVS/lh.resample.white
mris_resample --atlas_reg /usr/local/freesurfer/subjects/SynthF/surf/lh.sphere --annot_in /usr/local/freesurfer/subjects/SynthN/label/lh.aparc.annot --annot_out CVS/lh.resample.aparc.annot --subject_surf /usr/local/freesurfer/subjects/SynthN/surf/lh.pial --subject_reg /usr/local/freesurfer/subjects/SynthN/surf/lh.cvs.toSynthF.sphere.reg --out CVS/lh.resample.pial
mris_resample --atlas_reg /usr/local/freesurfer/subjects/SynthF/surf/rh.sphere --annot_in /usr/local/freesurfer/subjects/SynthN/label/rh.aparc.annot --annot_out CVS/rh.resample.aparc.annot --subject_surf /usr/local/freesurfer/subjects/SynthN/surf/rh.white --subject_reg /usr/local/freesurfer/subjects/SynthN/surf/rh.cvs.toSynthF.sphere.reg --out CVS/rh.resample.white
mris_resample --atlas_reg /usr/local/freesurfer/subjects/SynthF/surf/rh.sphere --annot_in /usr/local/freesurfer/subjects/SynthN/label/rh.aparc.annot --annot_out CVS/rh.resample.aparc.annot --subject_surf /usr/local/freesurfer/subjects/SynthN/surf/rh.pial --subject_reg /usr/local/freesurfer/subjects/SynthN/surf/rh.cvs.toSynthF.sphere.reg --out CVS/rh.resample.pial
mri_cvs_register: Step 1 (spherical registration) took 4010 seconds
Ready for elastic registration (CVS: Step 2)
surf2vol -fixed_mri /usr/local/freesurfer/subjects/SynthF/mri//norm.mgz -moving_mri /usr/local/freesurfer/subjects/SynthN/mri//norm.mgz -fixed_surf /usr/local/freesurfer/subjects/SynthF/surf//lh.white -moving_surf CVS/lh.resample.white -fixed_surf_2 /usr/local/freesurfer/subjects/SynthF/surf//rh.white -moving_surf_2 CVS/rh.resample.white -fixed_surf_3 /usr/local/freesurfer/subjects/SynthF/surf//lh.pial -moving_surf_3 CVS/lh.resample.pial -fixed_surf_4 /usr/local/freesurfer/subjects/SynthF/surf//rh.pial -moving_surf_4 CVS/rh.resample.pial -aparc /usr/local/freesurfer/subjects/SynthF/label//lh.aparc.annot -aparc_2 /usr/local/freesurfer/subjects/SynthF/label//rh.aparc.annot -aparc_3 /usr/local/freesurfer/subjects/SynthF/label//lh.aparc.annot -aparc_4 /usr/local/freesurfer/subjects/SynthF/label//rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -penalty_weight 1000 -fem_steps 17 -elt_vol_range 5.0,10.0 -topology_old -compress -pc_type jacobi -ksp_type preonly -ksp_view -ksp_converged_reason -poisson .3 -young 1000 -cache_transform CVS/transform.txt -out CVS/el_reg_toSynthF.mgz -out_mesh CVS/el_reg_toSynthF -out_affine CVS/el_reg_toSynthF.affine.mgz
mri_cvs_register: Step 2 (elastic registration) took 2048 seconds
applyMorph --template /usr/local/freesurfer/subjects/SynthF/mri//aseg.mgz --transform CVS/el_reg_toSynthF.tm3d vol /usr/local/freesurfer/subjects/SynthN/mri//aseg.mgz CVS/el_reg_toSynthF_aseg.mgz nearest
Ready for volumetric registration (CVS: Step 3)
mri_nl_align -noneg -1 -passes 3 -z -1 -aseg -dtrans .1 -apply 1 -sigma .25 -intensity 0.0 -fixed -dt 0.25 -m 0.25 -T /usr/local/freesurfer/bin/id.xfm CVS/el_reg_toSynthF_aseg.mgz /usr/local/freesurfer/subjects/SynthF/mri//aseg.mgz CVS/nlalign-aseg.m3z
createMorph --out CVS/combined_toSynthF_elreg_aseg.tm3d --template /usr/local/freesurfer/subjects/SynthF/mri//aseg.mgz --subject /usr/local/freesurfer/subjects/SynthN/mri//aseg.mgz --in gcam CVS/nlalign-aseg.m3z morph CVS/el_reg_toSynthF.tm3d
exportGcam --fixed /usr/local/freesurfer/subjects/SynthF/mri//aseg.mgz --moving /usr/local/freesurfer/subjects/SynthN/mri//aseg.mgz --morph CVS/combined_toSynthF_elreg_aseg.tm3d --out_gcam CVS/combined_toSynthF_elreg_aseg.m3z
mri_vol2vol --targ /usr/local/freesurfer/subjects/SynthF/mri//aseg.mgz --m3z CVS/combined_toSynthF_elreg_aseg.m3z --noDefM3zPath --mov /usr/local/freesurfer/subjects/SynthN/mri//aseg.mgz --o CVS/step1_CVSmorphed_toSynthF_aseg.mgz --interp nearest --no-save-reg
mri_vol2vol --targ /usr/local/freesurfer/subjects/SynthF/mri//norm.mgz --m3z CVS/combined_toSynthF_elreg_aseg.m3z --noDefM3zPath --mov /usr/local/freesurfer/subjects/SynthN/mri//norm.mgz --o CVS/step1_CVSmorphed_toSynthF_norm.mgz --interp trilin --no-save-reg
mri_nl_align -renormalize 1 -apply 1 -z 1 -sigma 2 -dt 0.0001 -intensity 0.1 -T /usr/local/freesurfer/bin/id.xfm CVS/step1_CVSmorphed_toSynthF_norm.mgz /usr/local/freesurfer/subjects/SynthF/mri//norm.mgz CVS/nlalign-afteraseg-norm.m3z
createMorph --out CVS/combined_toSynthF_elreg_afteraseg-norm.tm3d --template /usr/local/freesurfer/subjects/SynthF/mri//norm.mgz --subject /usr/local/freesurfer/subjects/SynthN/mri//norm.mgz --in gcam CVS/nlalign-afteraseg-norm.m3z morph CVS/combined_toSynthF_elreg_aseg.tm3d
exportGcam --fixed /usr/local/freesurfer/subjects/SynthF/mri//norm.mgz --moving /usr/local/freesurfer/subjects/SynthN/mri//norm.mgz --morph CVS/combined_toSynthF_elreg_afteraseg-norm.tm3d --out_gcam CVS/combined_toSynthF_elreg_afteraseg-norm.m3z
rm -f CVS/combined_toSynthF_elreg_aseg.tm3d CVS/combined_toSynthF_elreg_afteraseg-norm.tm3d
mri_vol2vol --targ /usr/local/freesurfer/subjects/SynthF/mri//norm.mgz --m3z CVS/combined_toSynthF_elreg_afteraseg-norm.m3z --noDefM3zPath --mov /usr/local/freesurfer/subjects/SynthN/mri//norm.mgz --o CVS/final_CVSmorphed_toSynthF_norm.mgz --no-save-reg
mri_vol2vol --targ /usr/local/freesurfer/subjects/SynthF/mri//aseg.mgz --m3z CVS/combined_toSynthF_elreg_afteraseg-norm.m3z --noDefM3zPath --mov /usr/local/freesurfer/subjects/SynthN/mri//aseg.mgz --o CVS/final_CVSmorphed_toSynthF_aseg.mgz --interp nearest --no-save-reg
mri_cvs_register: Step 3 (volumetric registration) took 39193 seconds
mv CVS/combined_toSynthF_elreg_afteraseg-norm.m3z CVS/final_CVSmorph_toSynthF.m3z
rm -f CVS/nlalign-afteraseg-norm.m3z CVS/nlalign-aseg.m3z CVS/combined_toSynthF_elreg_aseg.m3z
rm -f CVS/el_reg_toSynthF.tm3d
Finished with the cvs-registration pipeline.
 
Started at Wed 14 Dec 20:40:38 GMT 2016
Ended at Thu 15 Dec 09:14:49 GMT 2016
 
mri_cvs_register Done