mri_convert -c /g/data/ey6/keshuo/strokog/sss/edit_version/stroke_3_month/T1/000216RRW_T1.nii /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz reading from /g/data/ey6/keshuo/strokog/sss/edit_version/stroke_3_month/T1/000216RRW_T1.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.997617, 0.0402583, 0.0560287) j_ras = (-0.0245283, 0.966003, -0.257364) k_ras = (-0.064485, 0.255376, 0.964689) Reslicing using trilinear interpolation writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz... mri_convert -c /g/data/ey6/keshuo/strokog/sss/edit_version/stroke_3_year/T1/000216RRW_T1.nii /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz reading from /g/data/ey6/keshuo/strokog/sss/edit_version/stroke_3_year/T1/000216RRW_T1.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999213, 0.0370813, 0.0140537) j_ras = (-0.0324895, 0.96872, -0.24602) k_ras = (-0.0227368, 0.24537, 0.969163) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 630 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz... mri_convert -c /g/data/ey6/keshuo/strokog/sss/edit_version/stroke_5_year/T1/000216RRW_T1_COR.nii /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz reading from /g/data/ey6/keshuo/strokog/sss/edit_version/stroke_5_year/T1/000216RRW_T1_COR.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998502, 0.0457279, 0.0300568) j_ras = (-0.0354035, 0.958655, -0.28236) k_ras = (-0.0417258, 0.280873, 0.958837) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 642 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.39698e-09, 1.86265e-09) j_ras = (-1.86265e-09, 2.98023e-08, -1) k_ras = (3.25963e-09, 1, 1.49012e-08) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz... Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 2.98023e-08, -1) k_ras = (0, 1, 0) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz... Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz... mri_convert -c /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997617, -0.0402583, -0.0560287) j_ras = (0.064485, -0.255376, -0.964689) k_ras = (-0.0245283, 0.966003, -0.257364) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 110 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999213, -0.0370813, -0.0140537) j_ras = (0.0227368, -0.24537, -0.969163) k_ras = (-0.0324895, 0.96872, -0.24602) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz... changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 110 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998502, -0.0457279, -0.0300568) j_ras = (0.0417258, -0.280873, -0.958837) k_ras = (-0.0354035, 0.958655, -0.28236) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz... changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 110 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz... mri_convert -c /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997617, -0.0402583, -0.0560287) j_ras = (0.064485, -0.255376, -0.964689) k_ras = (-0.0245283, 0.966003, -0.257364) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 255 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.presurf.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.presurf.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.presurf.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999213, -0.0370813, -0.0140537) j_ras = (0.0227368, -0.24537, -0.969163) k_ras = (-0.0324895, 0.96872, -0.24602) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz... changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 255 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.presurf.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.presurf.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.presurf.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.presurf.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998502, -0.0457279, -0.0300568) j_ras = (0.0417258, -0.280873, -0.958837) k_ras = (-0.0354035, 0.958655, -0.28236) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.presurf.mgz... changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 255 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.presurf.mgz... mri_convert -c /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997617, -0.0402583, -0.0560287) j_ras = (0.064485, -0.255376, -0.964689) k_ras = (-0.0245283, 0.966003, -0.257364) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 60 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.auto_noCCseg.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.auto_noCCseg.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.auto_noCCseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999213, -0.0370813, -0.0140537) j_ras = (0.0227368, -0.24537, -0.969163) k_ras = (-0.0324895, 0.96872, -0.24602) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz... changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 60 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/aseg.auto_noCCseg.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.auto_noCCseg.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.auto_noCCseg.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.auto_noCCseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998502, -0.0457279, -0.0300568) j_ras = (0.0417258, -0.280873, -0.958837) k_ras = (-0.0354035, 0.958655, -0.28236) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/aseg.auto_noCCseg.mgz... changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 60 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/aseg.auto_noCCseg.mgz... mri_convert -c /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997617, -0.0402583, -0.0560287) j_ras = (0.064485, -0.255376, -0.964689) k_ras = (-0.0245283, 0.966003, -0.257364) Reslicing using trilinear interpolation writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/wm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/wm.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/wm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999213, -0.0370813, -0.0140537) j_ras = (0.0227368, -0.24537, -0.969163) k_ras = (-0.0324895, 0.96872, -0.24602) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz... Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/wm.mgz... mri_convert -rl /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz -rt nearest /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/wm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/wm.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/wm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998502, -0.0457279, -0.0300568) j_ras = (0.0417258, -0.280873, -0.958837) k_ras = (-0.0354035, 0.958655, -0.28236) reading template info from volume /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/wm.mgz... Reslicing using nearest writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/wm.mgz... INFO: SUBJECTS_DIR is /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime Actual FREESURFER_HOME /g/data/ey6/keshuo/my_software/freesurfer/freesurfer Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Longitudinal Base Subject Creation Wed Mar 13 03:15:26 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template rca-base-init -base 000216RRW_template -tp 000216RRW_tp1 -tp 000216RRW_tp2 -tp 000216RRW_tp3 -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/scripts/recon-all-status.log Wed Mar 13 03:15:26 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/rca-base-init -base 000216RRW_template -tp 000216RRW_tp1 -tp 000216RRW_tp2 -tp 000216RRW_tp3 -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/scripts/recon-all-status.log freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 rca-base-init 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2239854 #-------------------------------------------- #@# Longitudinal Base Subject Creation Wed Mar 13 03:15:26 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template mri_diff --notallow-pix --notallow-geo /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/rawavg.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/rawavg.mgz @#@FSTIME 2024:03:13:03:15:26 mri_diff N 4 e 0.22 S 0.03 U 1.14 P 522% M 38244 F 25 R 9055 W 0 c 7 w 94 I 3616 O 0 L 2.68 2.25 2.14 @#@FSLOADPOST 2024:03:13:03:15:26 mri_diff N 4 2.68 2.25 2.14 mri_diff --notallow-pix --notallow-geo /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/rawavg.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/rawavg.mgz @#@FSTIME 2024:03:13:03:15:26 mri_diff N 4 e 0.21 S 0.14 U 1.10 P 592% M 38252 F 4 R 9076 W 0 c 14 w 54 I 0 O 0 L 2.68 2.25 2.14 @#@FSLOADPOST 2024:03:13:03:15:27 mri_diff N 4 2.68 2.25 2.14 mri_robust_template --mov /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz --lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta --template /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/norm_template.mgz --average 1 --sat 4.685 7.4.1 --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz as movable/source volume. --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz as movable/source volume. --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz as movable/source volume. Total: 3 input volumes --lta: Will output LTA transforms --template: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 Will use TP 1 as random initial target (seed 5271 ). MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz ) to TP 1 ( /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz ) [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz ) to TP 1 ( /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz ) * WARNING: TP 3 to 1 did not converge !! Input rotation's max deviation from rotation is: 2.92815e-07 Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! Cosines of input transforms not identical ! computing mean coord of TP 1 ( /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/norm.mgz ) mapping back to rot, err = 1.35974e-16 computing mean coord of TP 2 ( /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/norm.mgz ) mapping back to rot, err = 8.49537e-08 computing mean coord of TP 3 ( /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/norm.mgz ) mapping back to rot, err = 1.46407e-07 Computing first template mapping movs and creating initial template... using median -- Template : (1, 1, 1)mm and (256, 256, 256) voxels. ======================================================= Working on global iteration : 1 ======================================================= noxformits = 3 Working on TP 1 Working on TP 2 Working on TP 3 - running multi-resolutional registration on TP 2... - running multi-resolutional registration on TP 1... - running multi-resolutional registration on TP 3... *** WARNING: TP 3 to template did not converge *** tp 2 distance: 0.0123858 tp 1 distance: 0.0148578 - mapping tp 2 to template (cubic bspline) ... tp 3 distance: 0.0590558 - mapping tp 1 to template (cubic bspline) ... - mapping tp 3 to template (cubic bspline) ... Finished TP : 1 ===================================================== Finished TP : 2 ===================================================== Finished TP : 3 ===================================================== Global Iteration 1 Distances: 0.0148578 0.0123858 0.0590558 Maxchange: 0.0590558 Computing new template 1 using median -- Template : (1, 1, 1)mm and (256, 256, 256) voxels. ======================================================= Working on global iteration : 2 ======================================================= noxformits = 1 Working on TP 1 Working on TP 3 Working on TP 2 - running multi-resolutional registration on TP 3... *** WARNING: TP 3 to template did not converge *** - running multi-resolutional registration on TP 1... - running multi-resolutional registration on TP 2... tp 3 distance: 0.028351 tp 1 distance: 0.0139394 - mapping tp 3 to template (cubic bspline) ... tp 2 distance: 0.0128021 - mapping tp 1 to template (cubic bspline) ... - mapping tp 2 to template (cubic bspline) ... Finished TP : 1 ===================================================== Finished TP : 2 ===================================================== Finished TP : 3 ===================================================== Global Iteration 2 Distances: 0.0139394 0.0128021 0.028351 Maxchange: 0.028351 Computing new template 2 using median -- Template : (1, 1, 1)mm and (256, 256, 256) voxels. DONE : computeTemplate Writing final template: /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/norm_template.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 3 minutes and 28 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf @#@FSTIME 2024:03:13:03:15:27 mri_robust_template N 14 e 207.94 S 12.23 U 244.71 P 123% M 1637944 F 9 R 9399230 W 0 c 828 w 1385 I 0 O 2072 L 2.68 2.25 2.14 @#@FSLOADPOST 2024:03:13:03:18:55 mri_robust_template N 14 3.32 2.94 2.47 mri_robust_template --mov /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig.mgz --average 1 --ixforms /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta --noit --template /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/orig.mgz 7.4.1 --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig.mgz as movable/source volume. --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig.mgz as movable/source volume. --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --template: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/orig.mgz as template output volume. reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 mapping movs and creating initial template... using median -- Template : (1, 1, 1)mm and (256, 256, 256) voxels. Writing final template: /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/orig.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 19 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf @#@FSTIME 2024:03:13:03:18:55 mri_robust_template N 13 e 19.32 S 0.24 U 22.44 P 117% M 320272 F 0 R 139870 W 0 c 371 w 250 I 0 O 9464 L 3.32 2.94 2.47 @#@FSLOADPOST 2024:03:13:03:19:14 mri_robust_template N 13 3.23 2.94 2.48 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms mri_concatenate_lta -invert1 000216RRW_tp1_to_000216RRW_template.lta identity.nofile 000216RRW_template_to_000216RRW_tp1.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file 000216RRW_template_to_000216RRW_tp1.lta... mri_concatenate_lta successful. @#@FSTIME 2024:03:13:03:19:14 mri_concatenate_lta N 4 e 0.02 S 0.01 U 0.00 P 50% M 3820 F 15 R 454 W 0 c 0 w 47 I 3600 O 8 L 3.23 2.94 2.48 @#@FSLOADPOST 2024:03:13:03:19:14 mri_concatenate_lta N 4 3.23 2.94 2.48 mri_concatenate_lta -invert1 000216RRW_tp2_to_000216RRW_template.lta identity.nofile 000216RRW_template_to_000216RRW_tp2.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file 000216RRW_template_to_000216RRW_tp2.lta... mri_concatenate_lta successful. @#@FSTIME 2024:03:13:03:19:14 mri_concatenate_lta N 4 e 0.01 S 0.00 U 0.00 P 66% M 3796 F 0 R 467 W 0 c 0 w 32 I 0 O 8 L 3.23 2.94 2.48 @#@FSLOADPOST 2024:03:13:03:19:14 mri_concatenate_lta N 4 3.23 2.94 2.48 mri_concatenate_lta -invert1 000216RRW_tp3_to_000216RRW_template.lta identity.nofile 000216RRW_template_to_000216RRW_tp3.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file 000216RRW_template_to_000216RRW_tp3.lta... mri_concatenate_lta successful. @#@FSTIME 2024:03:13:03:19:14 mri_concatenate_lta N 4 e 0.01 S 0.00 U 0.00 P 66% M 3776 F 0 R 467 W 0 c 0 w 31 I 0 O 8 L 3.23 2.94 2.48 @#@FSLOADPOST 2024:03:13:03:19:14 mri_concatenate_lta N 4 3.23 2.94 2.48 Preparing for skull stripping mri_robust_template --mov /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/brainmask.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/brainmask.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/brainmask.mgz --average 0 --ixforms /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta --noit --finalnearest --template /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/brainmask_template.mgz 7.4.1 --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/brainmask.mgz as movable/source volume. --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/brainmask.mgz as movable/source volume. --mov: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/brainmask.mgz as movable/source volume. Total: 3 input volumes --average: Using method 0 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --finalnearest: Use nearest neighbor interpolation for final average! --template: Using /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/brainmask_template.mgz as template output volume. reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/brainmask.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/brainmask.mgz' to bspline ... MRItoBSpline degree 3 reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/brainmask.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/brainmask.mgz' to bspline ... MRItoBSpline degree 3 reading source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/brainmask.mgz'... converting source '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/brainmask.mgz' to bspline ... MRItoBSpline degree 3 mapping movs and creating initial template... using mean -- Template : (1, 1, 1)mm and (256, 256, 256) voxels. Writing final template: /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/brainmask_template.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 8 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf @#@FSTIME 2024:03:13:03:19:14 mri_robust_template N 14 e 8.21 S 0.46 U 8.91 P 114% M 593196 F 5 R 235319 W 0 c 78 w 742 I 28328 O 9608 L 3.23 2.94 2.48 @#@FSLOADPOST 2024:03:13:03:19:23 mri_robust_template N 14 3.21 2.94 2.48 Started at Wed Mar 13 03:15:26 AEDT 2024 Ended at Wed Mar 13 03:19:23 AEDT 2024 rca-base-init Done #-------------------------------------------- #@# MotionCor Wed Mar 13 03:19:23 AEDT 2024 #-------------------------------------------- #@# Talairach Wed Mar 13 03:19:23 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /bin/bc /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux Wed Mar 13 03:19:23 AEDT 2024 tmpdir is ./tmp.mri_nu_correct.mni.2240243 cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2240243/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.2240243/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2240243/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2240243/nu0.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.17309e-09, 2.56114e-09) j_ras = (-2.56114e-09, 2.48353e-09, -1) k_ras = (-2.17309e-09, 1, 2.48353e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Wed Mar 13 03:22:15 AEDT 2024 mri_nu_correct.mni done @#@FSTIME 2024:03:13:03:19:23 mri_nu_correct.mni N 12 e 171.84 S 0.50 U 171.94 P 100% M 503256 F 10 R 149293 W 0 c 15 w 765 I 8936 O 17424 L 3.21 2.94 2.48 @#@FSLOADPOST 2024:03:13:03:22:15 mri_nu_correct.mni N 12 3.03 3.00 2.59 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Wed Mar 13 03:22:15 AEDT 2024 Ended at Wed Mar 13 03:22:34 AEDT 2024 talairach_avi done @#@FSTIME 2024:03:13:03:22:15 talairach_avi N 4 e 19.66 S 1.54 U 12.44 P 71% M 255192 F 145 R 403038 W 0 c 23 w 2586 I 275648 O 295272 L 3.03 3.00 2.59 @#@FSLOADPOST 2024:03:13:03:22:34 talairach_avi N 4 2.95 2.98 2.59 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.4.1 --src: orig.mgz src image (geometry). --trg: /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.10987 -0.00489 0.00112 1.02765; 0.02240 1.12064 -0.00430 3.11215; -0.01165 -0.03217 1.21730 -0.02284; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri #-------------------------------------------- #@# Talairach Failure Detection Wed Mar 13 03:22:36 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7461, pval=0.6675 >= threshold=0.0050) @#@FSTIME 2024:03:13:03:22:37 talairach_afd N 4 e 0.03 S 0.01 U 0.00 P 33% M 4100 F 46 R 421 W 0 c 0 w 78 I 7216 O 0 L 2.95 2.98 2.59 @#@FSLOADPOST 2024:03:13:03:22:37 talairach_afd N 4 2.95 2.98 2.59 awk -f /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/extract_talairach_avi_QA.awk /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/talairach_avi.log tal_QC_AZS /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/talairach_avi.log TalAviQA: 0.97447 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Mar 13 03:22:37 AEDT 2024 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /bin/bc /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux Wed Mar 13 03:22:37 AEDT 2024 tmpdir is ./tmp.mri_nu_correct.mni.2240530 cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2240530/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.2240530/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2240530/ones.mgz 7.4.1 cwd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.2240530/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2240530/ones.mgz sysname Linux hostname gadi-cpu-clx-0727.gadi.nci.org.au machine x86_64 user kl5945 input ./tmp.mri_nu_correct.mni.2240530/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2240530/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.2240530/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2240530/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2240530/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2240530/input.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2240530/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2240530/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2240530/input.mean.dat sysname Linux hostname gadi-cpu-clx-0727.gadi.nci.org.au machine x86_64 user kl5945 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2240530/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.2240530/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2240530/ones.mgz --i ./tmp.mri_nu_correct.mni.2240530/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2240530/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2240530/output.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2240530/ones.mgz --i ./tmp.mri_nu_correct.mni.2240530/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2240530/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2240530/output.mean.dat sysname Linux hostname gadi-cpu-clx-0727.gadi.nci.org.au machine x86_64 user kl5945 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2240530/ones.mgz Loading ./tmp.mri_nu_correct.mni.2240530/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.2240530/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2240530/nu0.mgz ./tmp.mri_nu_correct.mni.2240530/nu0.mgz mul 1.23940801902036294792 Saving result to './tmp.mri_nu_correct.mni.2240530/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2240530/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2240530/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.2240530/nu0.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.17309e-09, 2.56114e-09) j_ras = (-2.56114e-09, 2.48353e-09, -1) k_ras = (-2.17309e-09, 1, 2.48353e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 5 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 5, i2 = 37 #mri_make_uchar# mapping 11 81 to 3 110 : b -14.2391 m 1.52488 : thresh 9.33784 maxsat 176.564 : nzero 12622519 nsat 48738 Wed Mar 13 03:25:46 AEDT 2024 mri_nu_correct.mni done @#@FSTIME 2024:03:13:03:22:37 mri_nu_correct.mni N 9 e 188.93 S 3.29 U 194.41 P 104% M 612136 F 199 R 824543 W 0 c 108 w 2663 I 18976 O 41800 L 2.95 2.98 2.59 @#@FSLOADPOST 2024:03:13:03:25:46 mri_nu_correct.mni N 9 3.12 3.06 2.70 mri_add_xform_to_header -c /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2024:03:13:03:25:46 mri_add_xform_to_header N 4 e 0.40 S 0.05 U 0.96 P 252% M 21536 F 65 R 4847 W 0 c 6 w 151 I 6488 O 6880 L 3.12 3.06 2.70 @#@FSLOADPOST 2024:03:13:03:25:46 mri_add_xform_to_header N 4 3.12 3.06 2.70 #-------------------------------------------- #@# Intensity Normalization Wed Mar 13 03:25:46 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri mri_normalize -g 1 -seed 1234 -mprage -W ctrl_vol.mgz bias_vol.mgz nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE writing ctrl pts to ctrl_vol.mgz writing bias field to bias_vol.mgz reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.10987 -0.00489 0.00112 1.02765; 0.02240 1.12064 -0.00430 3.11215; -0.01165 -0.03217 1.21730 -0.02284; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 writing control point volume to ctrl_vol.mgz... writing control point volume to ctrl_vol.mgz... writing control point volume to ctrl_vol.mgz... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 109 white matter peak found at 89 gm peak at 71 (71), valley at 59 (59) csf peak at 36, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 69 (69), valley at 26 (26) csf peak at 35, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing bias field to bias_vol.mgz.... writing output to T1.mgz 3D bias adjustment took 1 minutes and 19 seconds. @#@FSTIME 2024:03:13:03:25:46 mri_normalize N 10 e 79.02 S 0.60 U 90.63 P 115% M 580072 F 43 R 524128 W 0 c 34 w 248 I 4728 O 35560 L 3.12 3.06 2.70 @#@FSLOADPOST 2024:03:13:03:27:05 mri_normalize N 10 3.62 3.31 2.83 #-------------------------------------------- #@# Skull Stripping Wed Mar 13 03:27:05 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri mri_mask -keep_mask_deletion_edits T1.mgz brainmask_template.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 maskval=0, outval=0 Writing masked volume to brainmask.auto.mgz...done. @#@FSTIME 2024:03:13:03:27:05 mri_mask N 4 e 1.03 S 0.21 U 2.13 P 226% M 187144 F 24 R 46393 W 0 c 18 w 158 I 4176 O 2096 L 3.62 3.31 2.83 @#@FSLOADPOST 2024:03:13:03:27:06 mri_mask N 4 3.62 3.31 2.83 mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_template.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 maskval=255, outval=255 Writing masked volume to brainmask.auto.mgz...done. @#@FSTIME 2024:03:13:03:27:06 mri_mask N 6 e 1.03 S 0.19 U 2.09 P 221% M 187148 F 3 R 46414 W 0 c 11 w 120 I 0 O 2096 L 3.62 3.31 2.83 @#@FSLOADPOST 2024:03:13:03:27:07 mri_mask N 6 3.62 3.31 2.83 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Mar 13 03:27:08 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri mri_em_register -mask brainmask.mgz norm_template.mgz /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 20 == reading 1 input volumes... logging results to talairach.log reading '/g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'norm_template.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 78.8 (495 zeros) ************************************************ spacing=8, using 2251 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2251, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (60, 75, 49) --> (192, 152, 202) finding center of left hemi white matter using (104, 101, 126) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (88,92,107) --> (120, 110,144) to find MRI wm before smoothing, mri peak at 239 robust fit to distribution - 161 +- 19.4 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -5.360 ************************************************ First Search limited to translation only. ************************************************ max log p = -5.293346 @ (-10.526, -10.526, -10.526) max log p = -5.277543 @ (15.789, -5.263, -5.263) max log p = -5.255336 @ (-7.895, 2.632, -2.632) max log p = -5.240447 @ (1.316, 1.316, 3.947) max log p = -5.233213 @ (0.658, 4.605, -0.658) max log p = -5.226485 @ (5.592, 0.987, -2.303) max log p = -5.226485 @ (0.000, 0.000, 0.000) max log p = -5.226485 @ (0.000, 0.000, 0.000) Found translation: (4.9, -6.3, -17.4): log p = -5.226 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-5.226, old_max_log_p =-5.226 (thresh=-5.2) 1.00000 0.00000 0.00000 4.93421; 0.00000 1.00000 0.00000 -6.25000; 0.00000 0.00000 1.00000 -17.43421; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-5.201, old_max_log_p =-5.226 (thresh=-5.2) 0.97614 0.09318 -0.01015 -2.49216; -0.10578 1.03195 -0.20051 23.70344; -0.00869 0.18846 0.92575 -36.70021; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-5.201, old_max_log_p =-5.201 (thresh=-5.2) 0.97614 0.09318 -0.01015 -2.49216; -0.10578 1.03195 -0.20051 23.70344; -0.00869 0.18846 0.92575 -36.70021; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 7 seconds. **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-5.198, old_max_log_p =-5.201 (thresh=-5.2) 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2251 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; nsamples 2251 Quasinewton: input matrix 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -5.198 (old=-5.360) transform before final EM align: 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 246437 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; nsamples 246437 Quasinewton: input matrix 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 5.6 tol 0.000000 final transform: 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 1040020 FSRUNTIME@ mri_em_register 0.0142 hours 20 threads registration took 0 minutes and 51 seconds. @#@FSTIME 2024:03:13:03:27:08 mri_em_register N 5 e 51.33 S 0.75 U 541.30 P 1055% M 614600 F 40 R 634443 W 0 c 1306 w 2581 I 144616 O 16 L 3.62 3.31 2.83 @#@FSLOADPOST 2024:03:13:03:28:00 mri_em_register N 5 10.33 5.11 3.46 #-------------------------------------- #@# CA Normalize Wed Mar 13 03:28:00 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz norm_template.mgz /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from norm_template.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (60, 75, 49) --> (192, 152, 203) finding center of left hemi white matter using (104, 101, 126) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (88,92,107) --> (120, 110,144) to find MRI wm before smoothing, mri peak at 239 robust fit to distribution - 161 +- 19.4 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246437 sample points... INFO: compute sample coordinates transform 0.97729 0.09329 -0.01016 -2.64367; -0.10578 1.03195 -0.20051 23.70344; -0.00870 0.18868 0.92683 -36.86637; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (119, 66, 42) --> (189, 185, 220) Left_Cerebral_White_Matter: limiting intensities to 151.0 --> 132.0 14 of 14 (100.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (54, 63, 45) --> (124, 181, 222) Right_Cerebral_White_Matter: limiting intensities to 154.0 --> 132.0 13 of 13 (100.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (119, 138, 58) --> (167, 185, 118) finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (71, 138, 57) --> (119, 180, 119) finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (100, 138, 92) --> (137, 200, 131) using 27 total control points for intensity normalization... 0 of 0 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (119, 66, 42) --> (189, 185, 220) finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (54, 63, 45) --> (124, 181, 222) finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (119, 138, 58) --> (167, 185, 118) finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (71, 138, 57) --> (119, 180, 119) finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (100, 138, 92) --> (137, 200, 131) skipping region 2 with no control points detected finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (119, 66, 42) --> (189, 185, 220) finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (54, 63, 45) --> (124, 181, 222) finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (119, 138, 58) --> (167, 185, 118) finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (71, 138, 57) --> (119, 180, 119) finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (100, 138, 92) --> (137, 200, 131) skipping region 3 with no control points detected writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 23 seconds. @#@FSTIME 2024:03:13:03:28:00 mri_ca_normalize N 8 e 23.26 S 0.44 U 25.10 P 109% M 661660 F 40 R 522422 W 0 c 15 w 238 I 4408 O 808 L 10.33 5.11 3.46 @#@FSLOADPOST 2024:03:13:03:28:23 mri_ca_normalize N 8 8.25 4.97 3.45 #-------------------------------------- #@# CA Reg Wed Mar 13 03:28:23 AEDT 2024 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 20 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 5 level2 1 tsec 12.174 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 4 level2 1 tsec 11.188 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 3 level2 1 tsec 10.94 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 2 level2 1 tsec 10.421 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 1 level2 1 tsec 10.407 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 0 level2 1 tsec 9.487 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 GCAMregister done in 2.0562 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17690 (16) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28275 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18948 (93) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20755 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.31831 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11957 (102) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11429 (102) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14521 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14336 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13305 (70) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15761 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13537 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13487 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19040 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18871 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24248 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.35833 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12897 (85) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13127 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12974 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17796 (79) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10999 (80) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13215 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11941 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20775 (25) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13297 (21) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94777 ( 0) gca peak Left_Cerebral_White_Matter = 0.11429 (102) gca peak Left_Cerebral_Cortex = 0.14521 (59) gca peak Left_Lateral_Ventricle = 0.10253 (16) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Left_Cerebellum_White_Matter = 0.19040 (84) gca peak Left_Cerebellum_Cortex = 0.13537 (57) gca peak Left_Thalamus = 0.12897 (85) gca peak Left_Caudate = 0.15761 (71) gca peak Left_Putamen = 0.12974 (78) gca peak Left_Pallidum = 0.18948 (93) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) gca peak Brain_Stem = 0.10999 (80) gca peak Left_Hippocampus = 0.31831 (58) gca peak Left_Amygdala = 0.24248 (57) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_VentralDC = 0.11941 (89) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Cerebral_White_Matter = 0.11957 (102) gca peak Right_Cerebral_Cortex = 0.14336 (58) gca peak Right_Lateral_Ventricle = 0.17690 (16) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Cerebellum_White_Matter = 0.18871 (83) gca peak Right_Cerebellum_Cortex = 0.13487 (56) gca peak Right_Thalamus = 0.13127 (83) gca peak Right_Caudate = 0.13305 (70) gca peak Right_Putamen = 0.17796 (79) gca peak Right_Pallidum = 0.28275 (96) gca peak Right_Hippocampus = 0.20755 (55) gca peak Right_Amygdala = 0.35833 (56) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_VentralDC = 0.13215 (88) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 2.72022 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 5 level2 1 tsec 13.243 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 4 level2 1 tsec 12.531 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 3 level2 1 tsec 12.557 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 2 level2 1 tsec 12.01 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 1 level2 1 tsec 12.173 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 0 level2 1 tsec 10.877 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 GCAMregister done in 2.35513 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 5 level2 1 tsec 12.242 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 4 level2 1 tsec 12.106 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 3 level2 1 tsec 12.011 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 2 level2 1 tsec 11.901 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 1 level2 1 tsec 11.852 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 0 level2 1 tsec 11.268 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 label assignment complete, 0 changed (0.00%) GCAMregister done in 2.29112 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 5 level2 1 tsec 7.553 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 4 level2 1 tsec 6.373 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 3 level2 1 tsec 8.133 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 2 level2 1 tsec 8.057 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 1 level2 1 tsec 8.178 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 2.18651 #GCAMreg# pass 0 level1 0 level2 1 tsec 5.872 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 2.18651 GCAMregister done in 1.35355 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 1710 tmin = 0.6289 Calls to gcamLabelEnergy 1424 tmin = 0.405783 Calls to gcamJacobianEnergy 1710 tmin = 0.3322 Calls to gcamSmoothnessEnergy 1710 tmin = 1.23028 Calls to gcamLogLikelihoodTerm 108 tmin = 0.11245 Calls to gcamLabelTerm 84 tmin = 0.43645 Calls to gcamJacobianTerm 108 tmin = 0.125733 Calls to gcamSmoothnessTerm 108 tmin = 0.0403833 Calls to gcamComputeGradient 108 tmin = 1.657 Calls to gcamComputeMetricProperties 2079 tmin = 0.611483 mri_ca_register took 0 hours, 10 minutes and 59 seconds. #VMPC# mri_ca_register VmPeak 4123360 FSRUNTIME@ mri_ca_register 0.1831 hours 20 threads @#@FSTIME 2024:03:13:03:28:23 mri_ca_register N 9 e 659.15 S 5.07 U 4533.86 P 688% M 1322892 F 147 R 3500983 W 0 c 27795 w 118542 I 5024 O 57528 L 8.25 4.97 3.45 @#@FSLOADPOST 2024:03:13:03:39:22 mri_ca_register N 9 8.43 8.32 5.95 #-------------------------------------- #@# SubCort Seg Wed Mar 13 03:39:22 AEDT 2024 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname gadi-cpu-clx-0727.gadi.nci.org.au machine x86_64 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 20 == reading 1 input volumes reading classifier array from /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 8.15 Atlas used for the 3D morph was /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20380 (13) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26283 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15814 (97) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.27624 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28723 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07623 (103) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07837 (105) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10165 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11113 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.27796 (67) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14473 (69) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14301 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14610 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16309 (85) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15172 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30461 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.32293 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11083 (90) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11393 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08575 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08618 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08005 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12854 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15703 (87) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17522 (25) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17113 (14) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94777 ( 0) gca peak Left_Cerebral_White_Matter = 0.07837 (105) gca peak Left_Cerebral_Cortex = 0.10165 (58) gca peak Left_Lateral_Ventricle = 0.15521 (20) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Left_Cerebellum_White_Matter = 0.16309 (85) gca peak Left_Cerebellum_Cortex = 0.14301 (56) gca peak Left_Thalamus = 0.11083 (90) gca peak Left_Caudate = 0.14473 (69) gca peak Left_Putamen = 0.08575 (81) gca peak Left_Pallidum = 0.15814 (97) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) gca peak Brain_Stem = 0.08005 (78) gca peak Left_Hippocampus = 0.28723 (59) gca peak Left_Amygdala = 0.30461 (58) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_VentralDC = 0.15703 (87) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Cerebral_White_Matter = 0.07623 (103) gca peak Right_Cerebral_Cortex = 0.11113 (58) gca peak Right_Lateral_Ventricle = 0.20380 (13) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Cerebellum_White_Matter = 0.15172 (84) gca peak Right_Cerebellum_Cortex = 0.14610 (55) gca peak Right_Thalamus = 0.11393 (83) gca peak Right_Caudate = 0.27796 (67) gca peak Right_Putamen = 0.08618 (78) gca peak Right_Pallidum = 0.26283 (96) gca peak Right_Hippocampus = 0.27624 (56) gca peak Right_Amygdala = 0.32293 (57) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_VentralDC = 0.12854 (88) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20380 (13) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26283 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15814 (97) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.27624 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28723 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07623 (103) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07837 (105) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10165 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11113 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.27796 (67) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14473 (69) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14301 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14610 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16309 (85) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15172 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30461 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.32293 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11083 (90) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11393 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08575 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08618 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08005 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12854 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15703 (87) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17522 (25) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17113 (14) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94777 ( 0) gca peak Left_Cerebral_White_Matter = 0.07837 (105) gca peak Left_Cerebral_Cortex = 0.10165 (58) gca peak Left_Lateral_Ventricle = 0.15521 (20) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Left_Cerebellum_White_Matter = 0.16309 (85) gca peak Left_Cerebellum_Cortex = 0.14301 (56) gca peak Left_Thalamus = 0.11083 (90) gca peak Left_Caudate = 0.14473 (69) gca peak Left_Putamen = 0.08575 (81) gca peak Left_Pallidum = 0.15814 (97) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) gca peak Brain_Stem = 0.08005 (78) gca peak Left_Hippocampus = 0.28723 (59) gca peak Left_Amygdala = 0.30461 (58) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_VentralDC = 0.15703 (87) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Cerebral_White_Matter = 0.07623 (103) gca peak Right_Cerebral_Cortex = 0.11113 (58) gca peak Right_Lateral_Ventricle = 0.20380 (13) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Cerebellum_White_Matter = 0.15172 (84) gca peak Right_Cerebellum_Cortex = 0.14610 (55) gca peak Right_Thalamus = 0.11393 (83) gca peak Right_Caudate = 0.27796 (67) gca peak Right_Putamen = 0.08618 (78) gca peak Right_Pallidum = 0.26283 (96) gca peak Right_Hippocampus = 0.27624 (56) gca peak Right_Amygdala = 0.32293 (57) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_VentralDC = 0.12854 (88) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 20815 voxels changed in iteration 0 of unlikely voxel relabeling 8 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 187 gm and wm labels changed (%100 to gray, % 0 to white out of all changed labels) 385 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 29602 changed. image ll: -5.300, PF=0.500 pass 2: 5348 changed. pass 3: 2738 changed. 16178 voxels changed in iteration 0 of unlikely voxel relabeling 32 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 8114 voxels changed in iteration 0 of unlikely voxel relabeling 18 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 7281 voxels changed in iteration 0 of unlikely voxel relabeling 48 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 13154 voxels changed in iteration 0 of unlikely voxel relabeling 42 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 9 with volume 28488 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 4 with volume 7117 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 7 with volume 26647 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 6113 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3564.802876 mri_ca_label stimesec 4.457723 mri_ca_label ru_maxrss 2142096 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 6736184 mri_ca_label ru_majflt 56 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 5320 mri_ca_label ru_oublock 592 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 2956 mri_ca_label ru_nivcsw 7416 mri_ca_label took 58 minutes and 4 seconds. mri_ca_label done @#@FSTIME 2024:03:13:03:39:22 mri_ca_label N 10 e 3484.39 S 4.57 U 3564.80 P 102% M 2142096 F 56 R 6736200 W 0 c 7416 w 2959 I 5320 O 592 L 8.43 8.32 5.95 @#@FSLOADPOST 2024:03:13:04:37:27 mri_ca_label N 10 3.08 3.14 3.17 #-------------------------------------- #@# CC Seg Wed Mar 13 04:37:27 AEDT 2024 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/cc_up.lta 000216RRW_template will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/cc_up.lta reading aseg from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/aseg.auto_noCCseg.mgz reading norm from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/norm.mgz 3089 voxels in left wm, 7676 in right wm, xrange [117, 126] searching rotation angles z=[-15 -1], y=[-9 5] searching scale 1 Z rot -14.6 searching scale 1 Z rot -14.3 searching scale 1 Z rot -14.1 searching scale 1 Z rot -13.8 searching scale 1 Z rot -13.6 searching scale 1 Z rot -13.3 searching scale 1 Z rot -13.1 searching scale 1 Z rot -12.8 searching scale 1 Z rot -12.6 searching scale 1 Z rot -12.3 searching scale 1 Z rot -12.1 searching scale 1 Z rot -11.8 searching scale 1 Z rot -11.6 searching scale 1 Z rot -11.3 searching scale 1 Z rot -11.1 searching scale 1 Z rot -10.8 searching scale 1 Z rot -10.6 searching scale 1 Z rot -10.3 searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 global minimum found at slice 120.0, rotations (-2.24, -7.33) final transformation (x=120.0, yr=-2.240, zr=-7.329): 0.99107 0.12756 -0.03876 -3.30594; -0.12746 0.99183 0.00498 1.71754; 0.03908 -0.00000 0.99924 -24.57617; 0.00000 0.00000 0.00000 1.00000; error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping Command exited with non-zero status 253 @#@FSTIME 2024:03:13:04:37:27 mri_cc N 7 e 17.40 S 0.28 U 18.29 P 106% M 224272 F 36 R 187395 W 0 c 24 w 141 I 4248 O 0 L 3.08 3.14 3.17 @#@FSLOADPOST 2024:03:13:04:37:44 mri_cc N 7 3.12 3.15 3.17 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 000216RRW_template exited with ERRORS at Wed Mar 13 04:37:44 AEDT 2024 For more details, see the log file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting fs-check-version --s 000216RRW_tp1.long.000216RRW_template --o /jobfs/110677042.gadi-pbs/tmp.kBFWqF Wed Mar 13 04:37:45 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/fs-check-version --s 000216RRW_tp1.long.000216RRW_template --o /jobfs/110677042.gadi-pbs/tmp.kBFWqF -rwxr-xr-x 1 kl5945 ey6 18565 Jun 14 2023 /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/fs-check-version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 $Id$ Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2241769 Current FS Version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Subject does not have a bstampfile, copying /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime Actual FREESURFER_HOME /g/data/ey6/keshuo/my_software/freesurfer/freesurfer Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux rca-long-tp-init -long 000216RRW_tp1 000216RRW_template -s 000216RRW_tp1.long.000216RRW_template -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/scripts/recon-all-status.log Wed Mar 13 04:37:46 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/rca-long-tp-init -long 000216RRW_tp1 000216RRW_template -s 000216RRW_tp1.long.000216RRW_template -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/scripts/recon-all-status.log freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 rca-long-tp-init 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2241946 longmc -long 000216RRW_tp1 000216RRW_template -s 000216RRW_tp1.long.000216RRW_template Wed Mar 13 04:37:46 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/longmc -long 000216RRW_tp1 000216RRW_template -s 000216RRW_tp1.long.000216RRW_template freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 longmc 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2242015 mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta -odt uchar -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri/orig.mgz mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta -odt uchar -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri/orig.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.49012e-08, -1) k_ras = (0, 1, 1.49012e-08) INFO: Reading transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99999 -0.00263 0.00421 0.72610; 0.00273 0.99969 -0.02488 -0.09477; -0.00414 0.02489 0.99968 -0.13034; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri/orig.mgz... mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri/rawavg.mgz mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri/rawavg.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.49012e-08, -1) k_ras = (0, 1, 1.49012e-08) INFO: Reading transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp1_to_000216RRW_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99999 -0.00263 0.00421 0.72610; 0.00273 0.99969 -0.02488 -0.09477; -0.00414 0.02489 0.99968 -0.13034; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri/rawavg.mgz... Started at Wed Mar 13 04:37:46 AEDT 2024 Ended at Wed Mar 13 04:38:00 AEDT 2024 Longmc-Run-Time-Sec 14 Longmc-Run-Time-Min 0.28 Longmc-Run-Time-Hours 0.00 longmc Done @#@FSTIME 2024:03:13:04:37:46 longmc N 5 e 13.87 S 0.26 U 14.79 P 108% M 104728 F 17 R 104710 W 0 c 48 w 692 I 592 O 17560 L 3.12 3.15 3.17 @#@FSLOADPOST 2024:03:13:04:38:00 longmc N 5 3.30 3.19 3.19 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/brainmask.mgz ./brainmask_000216RRW_template.mgz @#@FSTIME 2024:03:13:04:38:00 cp N 2 e 0.00 S 0.00 U 0.00 P 50% M 2944 F 0 R 384 W 0 c 0 w 14 I 0 O 2096 L 3.30 3.19 3.19 @#@FSLOADPOST 2024:03:13:04:38:00 cp N 2 3.30 3.19 3.19 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/mri cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/talairach.lta transforms/talairach.lta @#@FSTIME 2024:03:13:04:38:00 cp N 2 e 0.00 S 0.00 U 0.00 P 77% M 2176 F 0 R 122 W 0 c 0 w 14 I 0 O 8 L 3.30 3.19 3.19 @#@FSLOADPOST 2024:03:13:04:38:00 cp N 2 3.30 3.19 3.19 cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/aseg.mgz aseg_000216RRW_template.mgz cp: cannot stat '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/aseg.mgz': No such file or directory Command exited with non-zero status 1 @#@FSTIME 2024:03:13:04:38:00 cp N 2 e 0.00 S 0.00 U 0.00 P 100% M 2300 F 0 R 125 W 0 c 0 w 4 I 0 O 0 L 3.30 3.19 3.19 @#@FSLOADPOST 2024:03:13:04:38:00 cp N 2 3.30 3.19 3.19 ERROR: Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 000216RRW_tp1.long.000216RRW_template exited with ERRORS at Wed Mar 13 04:38:00 AEDT 2024 For more details, see the log file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp1.long.000216RRW_template/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting fs-check-version --s 000216RRW_tp2.long.000216RRW_template --o /jobfs/110677042.gadi-pbs/tmp.aI1QRu Wed Mar 13 04:38:01 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/fs-check-version --s 000216RRW_tp2.long.000216RRW_template --o /jobfs/110677042.gadi-pbs/tmp.aI1QRu -rwxr-xr-x 1 kl5945 ey6 18565 Jun 14 2023 /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/fs-check-version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 $Id$ Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2242265 Current FS Version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Subject does not have a bstampfile, copying /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime Actual FREESURFER_HOME /g/data/ey6/keshuo/my_software/freesurfer/freesurfer Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux rca-long-tp-init -long 000216RRW_tp2 000216RRW_template -s 000216RRW_tp2.long.000216RRW_template -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/scripts/recon-all-status.log Wed Mar 13 04:38:02 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/rca-long-tp-init -long 000216RRW_tp2 000216RRW_template -s 000216RRW_tp2.long.000216RRW_template -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/scripts/recon-all-status.log freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 rca-long-tp-init 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2242443 longmc -long 000216RRW_tp2 000216RRW_template -s 000216RRW_tp2.long.000216RRW_template Wed Mar 13 04:38:02 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/longmc -long 000216RRW_tp2 000216RRW_template -s 000216RRW_tp2.long.000216RRW_template freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 longmc 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2242512 mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta -odt uchar -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri/orig.mgz mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta -odt uchar -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri/orig.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.49012e-08, -1) k_ras = (0, 1, 1.49012e-08) INFO: Reading transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.00000 0.00165 -0.00012 0.81331; -0.00166 0.99990 -0.01375 -0.70508; 0.00009 0.01375 0.99991 1.04593; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri/orig.mgz... mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri/rawavg.mgz mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri/rawavg.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.49012e-08, -1) k_ras = (0, 1, 1.49012e-08) INFO: Reading transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp2_to_000216RRW_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.00000 0.00165 -0.00012 0.81331; -0.00166 0.99990 -0.01375 -0.70508; 0.00009 0.01375 0.99991 1.04593; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri/rawavg.mgz... Started at Wed Mar 13 04:38:02 AEDT 2024 Ended at Wed Mar 13 04:38:16 AEDT 2024 Longmc-Run-Time-Sec 14 Longmc-Run-Time-Min 0.28 Longmc-Run-Time-Hours 0.00 longmc Done @#@FSTIME 2024:03:13:04:38:02 longmc N 5 e 13.73 S 0.43 U 14.54 P 108% M 104744 F 1 R 107364 W 0 c 64 w 657 I 0 O 20368 L 3.30 3.19 3.19 @#@FSLOADPOST 2024:03:13:04:38:16 longmc N 5 3.23 3.18 3.18 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/brainmask.mgz ./brainmask_000216RRW_template.mgz @#@FSTIME 2024:03:13:04:38:16 cp N 2 e 0.00 S 0.00 U 0.00 P 66% M 2940 F 0 R 382 W 0 c 0 w 13 I 0 O 2096 L 3.23 3.18 3.18 @#@FSLOADPOST 2024:03:13:04:38:16 cp N 2 3.23 3.18 3.18 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/mri cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/talairach.lta transforms/talairach.lta @#@FSTIME 2024:03:13:04:38:16 cp N 2 e 0.01 S 0.00 U 0.00 P 70% M 2300 F 0 R 124 W 0 c 0 w 13 I 0 O 8 L 3.23 3.18 3.18 @#@FSLOADPOST 2024:03:13:04:38:16 cp N 2 3.23 3.18 3.18 cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/aseg.mgz aseg_000216RRW_template.mgz cp: cannot stat '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/aseg.mgz': No such file or directory Command exited with non-zero status 1 @#@FSTIME 2024:03:13:04:38:16 cp N 2 e 0.00 S 0.00 U 0.00 P 100% M 2108 F 0 R 121 W 0 c 0 w 4 I 0 O 0 L 3.23 3.18 3.18 @#@FSLOADPOST 2024:03:13:04:38:16 cp N 2 3.23 3.18 3.18 ERROR: Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 000216RRW_tp2.long.000216RRW_template exited with ERRORS at Wed Mar 13 04:38:16 AEDT 2024 For more details, see the log file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp2.long.000216RRW_template/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting fs-check-version --s 000216RRW_tp3.long.000216RRW_template --o /jobfs/110677042.gadi-pbs/tmp.sP5I4c Wed Mar 13 04:38:17 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/fs-check-version --s 000216RRW_tp3.long.000216RRW_template --o /jobfs/110677042.gadi-pbs/tmp.sP5I4c -rwxr-xr-x 1 kl5945 ey6 18565 Jun 14 2023 /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/fs-check-version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 $Id$ Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2242762 Current FS Version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Subject does not have a bstampfile, copying /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime Actual FREESURFER_HOME /g/data/ey6/keshuo/my_software/freesurfer/freesurfer Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux rca-long-tp-init -long 000216RRW_tp3 000216RRW_template -s 000216RRW_tp3.long.000216RRW_template -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/scripts/recon-all-status.log Wed Mar 13 04:38:18 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/rca-long-tp-init -long 000216RRW_tp3 000216RRW_template -s 000216RRW_tp3.long.000216RRW_template -log /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/scripts/recon-all.log -cf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/scripts/recon-all.cmd -sf /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/scripts/recon-all-status.log freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 rca-long-tp-init 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2242939 longmc -long 000216RRW_tp3 000216RRW_template -s 000216RRW_tp3.long.000216RRW_template Wed Mar 13 04:38:18 AEDT 2024 setenv SUBJECTS_DIR /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime cd /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template /g/data/ey6/keshuo/my_software/freesurfer/freesurfer/bin/longmc -long 000216RRW_tp3 000216RRW_template -s 000216RRW_tp3.long.000216RRW_template freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 longmc 7.4.1 Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2243008 mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta -odt uchar -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri/orig.mgz mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta -odt uchar -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri/orig.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.49012e-08, -1) k_ras = (0, 1, 1.49012e-08) INFO: Reading transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99999 0.00153 -0.00313 -1.57389; -0.00141 0.99927 0.03807 0.80119; 0.00318 -0.03807 0.99927 -0.90727; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri/orig.mgz... mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri/rawavg.mgz mri_convert -at /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta -rt cubic /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri/rawavg.mgz reading from /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.49012e-08, -1) k_ras = (0, 1, 1.49012e-08) INFO: Reading transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/000216RRW_tp3_to_000216RRW_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99999 0.00153 -0.00313 -1.57389; -0.00141 0.99927 0.03807 0.80119; 0.00318 -0.03807 0.99927 -0.90727; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri/rawavg.mgz... Started at Wed Mar 13 04:38:18 AEDT 2024 Ended at Wed Mar 13 04:38:32 AEDT 2024 Longmc-Run-Time-Sec 14 Longmc-Run-Time-Min 0.28 Longmc-Run-Time-Hours 0.00 longmc Done @#@FSTIME 2024:03:13:04:38:18 longmc N 5 e 13.67 S 0.34 U 14.47 P 108% M 104856 F 6 R 102908 W 0 c 363 w 646 I 0 O 20096 L 3.21 3.17 3.18 @#@FSLOADPOST 2024:03:13:04:38:32 longmc N 5 3.18 3.17 3.18 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/brainmask.mgz ./brainmask_000216RRW_template.mgz @#@FSTIME 2024:03:13:04:38:32 cp N 2 e 0.00 S 0.00 U 0.00 P 75% M 3000 F 0 R 381 W 0 c 0 w 13 I 0 O 2096 L 3.18 3.17 3.18 @#@FSLOADPOST 2024:03:13:04:38:32 cp N 2 3.18 3.17 3.18 /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/mri cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/talairach.lta transforms/talairach.lta @#@FSTIME 2024:03:13:04:38:32 cp N 2 e 0.00 S 0.00 U 0.00 P 50% M 2288 F 0 R 125 W 0 c 0 w 13 I 0 O 8 L 3.18 3.17 3.18 @#@FSLOADPOST 2024:03:13:04:38:32 cp N 2 3.18 3.17 3.18 cp /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/aseg.mgz aseg_000216RRW_template.mgz cp: cannot stat '/g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/aseg.mgz': No such file or directory Command exited with non-zero status 1 @#@FSTIME 2024:03:13:04:38:32 cp N 2 e 0.00 S 0.00 U 0.00 P 50% M 2232 F 0 R 123 W 0 c 0 w 4 I 0 O 0 L 3.18 3.17 3.18 @#@FSLOADPOST 2024:03:13:04:38:32 cp N 2 3.18 3.17 3.18 ERROR: Linux gadi-cpu-clx-0727.gadi.nci.org.au 4.18.0-513.11.1.el8.nci.x86_64 #1 SMP Thu Jan 18 16:42:37 AEDT 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 000216RRW_tp3.long.000216RRW_template exited with ERRORS at Wed Mar 13 04:38:32 AEDT 2024 For more details, see the log file /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_tp3.long.000216RRW_template/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ====================================================================================== Resource Usage on 2024-03-13 04:38:35: Job Id: 110677042.gadi-pbs Project: ey6 Exit Status: 1 Service Units: 89.55 NCPUs Requested: 20 NCPUs Used: 20 CPU Time Used: 02:39:26 Memory Requested: 128.0GB Memory Used: 2.63GB Walltime requested: 40:00:00 Walltime Used: 01:23:57 JobFS requested: 100.0MB JobFS used: 0B ======================================================================================