Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /execute Actual FREESURFER_HOME /usr/local/freesurfer Linux beec64fd34b7 4.15.0-1054-aws #56-Ubuntu SMP Thu Nov 7 16:15:59 UTC 2019 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/execute/freesurfer/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Thu Feb 27 15:29:57 UTC 2020 Found 1 runs /execute/freesurfer/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /execute/freesurfer/mri/orig/001.mgz /execute/freesurfer/mri/rawavg.mgz /execute/freesurfer mri_convert /execute/freesurfer/mri/rawavg.mgz /execute/freesurfer/mri/orig.mgz --conform mri_convert.bin /execute/freesurfer/mri/rawavg.mgz /execute/freesurfer/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /execute/freesurfer/mri/rawavg.mgz... TR=6.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999963, 0, -0.00863488) j_ras = (0, 1, 0) k_ras = (0.00863488, 0, 0.999963) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /execute/freesurfer/mri/orig.mgz... mri_add_xform_to_header -c /execute/freesurfer/mri/transforms/talairach.xfm /execute/freesurfer/mri/orig.mgz /execute/freesurfer/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Feb 27 15:30:11 UTC 2020 /execute/freesurfer/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /execute/freesurfer/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux beec64fd34b7 4.15.0-1054-aws #56-Ubuntu SMP Thu Nov 7 16:15:59 UTC 2019 x86_64 GNU/Linux Thu Feb 27 15:30:11 UTC 2020 Program nu_correct, built from: N3 1.12.00 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.929 /execute/freesurfer/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.929/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.929/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.929/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Feb 27 15:30:14 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.929/nu0.mnc ./tmp.mri_nu_correct.mni.929/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.929/0/ -iterations 1000 -distance 50 [docker@beec64fd34b7:/execute/freesurfer/mri/] [2020-02-27 15:30:14] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.929/0/ ./tmp.mri_nu_correct.mni.929/nu0.mnc ./tmp.mri_nu_correct.mni.929/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 62 CV of field change: 0.00097736 mri_convert ./tmp.mri_nu_correct.mni.929/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.929/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.929/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu Feb 27 15:31:47 UTC 2020 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu Feb 27 15:31:47 UTC 2020 Ended at Thu Feb 27 15:32:31 UTC 2020 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Feb 27 15:32:33 UTC 2020 /execute/freesurfer/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6710, pval=0.3663 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /execute/freesurfer/mri/transforms/talairach_avi.log tal_QC_AZS /execute/freesurfer/mri/transforms/talairach_avi.log TalAviQA: 0.96354 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Thu Feb 27 15:32:34 UTC 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /execute/freesurfer/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux beec64fd34b7 4.15.0-1054-aws #56-Ubuntu SMP Thu Nov 7 16:15:59 UTC 2019 x86_64 GNU/Linux Thu Feb 27 15:32:34 UTC 2020 Program nu_correct, built from: N3 1.12.00 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.1915 /execute/freesurfer/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1915/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1915/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1915/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Feb 27 15:32:36 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.1915/nu0.mnc ./tmp.mri_nu_correct.mni.1915/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1915/0/ [docker@beec64fd34b7:/execute/freesurfer/mri/] [2020-02-27 15:32:36] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1915/0/ ./tmp.mri_nu_correct.mni.1915/nu0.mnc ./tmp.mri_nu_correct.mni.1915/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 43 CV of field change: 0.000990058 -------------------------------------------------------- Iteration 2 Thu Feb 27 15:33:30 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.1915/nu1.mnc ./tmp.mri_nu_correct.mni.1915/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1915/1/ [docker@beec64fd34b7:/execute/freesurfer/mri/] [2020-02-27 15:33:30] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1915/1/ ./tmp.mri_nu_correct.mni.1915/nu1.mnc ./tmp.mri_nu_correct.mni.1915/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000984536 mri_binarize --i ./tmp.mri_nu_correct.mni.1915/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1915/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /execute/freesurfer/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1915/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1915/ones.mgz sysname Linux hostname beec64fd34b7 machine x86_64 user docker input ./tmp.mri_nu_correct.mni.1915/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.1915/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1915/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1915/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1915/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1915/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1915/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1915/input.mean.dat sysname Linux hostname beec64fd34b7 machine x86_64 user docker UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1915/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 0 Writing to ./tmp.mri_nu_correct.mni.1915/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1915/ones.mgz --i ./tmp.mri_nu_correct.mni.1915/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1915/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1915/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1915/ones.mgz --i ./tmp.mri_nu_correct.mni.1915/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1915/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1915/output.mean.dat sysname Linux hostname beec64fd34b7 machine x86_64 user docker UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1915/ones.mgz Loading ./tmp.mri_nu_correct.mni.1915/nu2.mnc 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 0 Writing to ./tmp.mri_nu_correct.mni.1915/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.1915/nu2.mnc ./tmp.mri_nu_correct.mni.1915/nu2.mnc mul 1.06404210353673649912 Saving result to './tmp.mri_nu_correct.mni.1915/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.1915/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.1915/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.1915/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) 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 6 seconds. mapping ( 8, 165) to ( 3, 110) Thu Feb 27 15:34:45 UTC 2020 mri_nu_correct.mni done mri_add_xform_to_header -c /execute/freesurfer/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Feb 27 15:34:46 UTC 2020 /execute/freesurfer/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.03017 0.02178 -0.01726 -4.77718; 0.04282 0.96438 0.21169 -33.07177; 0.00831 -0.28468 1.00439 -10.68317; 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 = 11 Starting OpenSpline(): npoints = 11 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 50 (50), valley at 32 (32) csf peak at 26, setting threshold to 42 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 110 gm peak at 47 (47), valley at 28 (28) csf peak at 24, setting threshold to 39 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 44 seconds. #-------------------------------------------- #@# Skull Stripping Thu Feb 27 15:36:31 UTC 2020 /execute/freesurfer/mri mri_em_register -rusage /execute/freesurfer/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (52, 19, 25) --> (202, 255, 245) using (102, 98, 135) as brain centroid... mean wm in atlas = 108, using box (84,69,108) --> (120, 127,162) to find MRI wm before smoothing, mri peak at 101 robust fit to distribution - 100 +- 18.7 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.564 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.385741 @ (-9.091, 9.091, -9.091) max log p = -4.232870 @ (4.545, 4.545, -4.545) max log p = -4.209099 @ (2.273, 2.273, -2.273) max log p = -4.209099 @ (0.000, 0.000, 0.000) max log p = -4.193285 @ (0.568, -1.705, 1.705) max log p = -4.193285 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 14.2, -14.2): log p = -4.193 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.088, old_max_log_p =-4.193 (thresh=-4.2) 1.07500 0.00000 0.00000 -11.19804; 0.00000 1.03837 0.27823 -18.02004; 0.00000 -0.27823 1.03837 24.09933; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.088, old_max_log_p =-4.088 (thresh=-4.1) 1.07500 0.00000 0.00000 -11.19804; 0.00000 1.03837 0.27823 -18.02004; 0.00000 -0.27823 1.03837 24.09933; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.015, old_max_log_p =-4.088 (thresh=-4.1) 1.05484 0.00000 0.00000 -10.52166; 0.00000 1.01890 0.27301 -15.01639; 0.00000 -0.26278 0.98069 23.36744; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.996, old_max_log_p =-4.015 (thresh=-4.0) 1.05428 0.03484 0.00825 -15.69209; -0.03451 1.06425 0.25208 -13.55055; 0.00000 -0.21411 0.93482 23.03922; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.996, old_max_log_p =-3.996 (thresh=-4.0) 1.05428 0.03484 0.00825 -15.69209; -0.03451 1.06425 0.25208 -13.55055; 0.00000 -0.21411 0.93482 23.03922; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.970, old_max_log_p =-3.996 (thresh=-4.0) 1.05325 0.02449 0.01398 -14.53056; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.967, old_max_log_p =-3.970 (thresh=-4.0) 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.967 (old=-4.564) transform before final EM align: 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.3 tol 0.000000 final transform: 1.05202 0.02446 0.01397 -14.36719; -0.02595 1.07163 0.23758 -13.78002; -0.00918 -0.19657 0.93765 22.20866; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1175.964531 mri_em_register stimesec 2.156834 mri_em_register ru_maxrss 614468 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 165812 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 150296 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 510 mri_em_register ru_nivcsw 13700 registration took 5 minutes and 33 seconds. mri_watershed -rusage /execute/freesurfer/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=131 y=108 z=115 r=100 first estimation of the main basin volume: 4279832 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=169, y=92, z=87, Imax=255 CSF=15, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=9613136057 voxels, voxel volume =1.000 = 9613136057 mmm3 = 9613135.872 cm3 done. PostAnalyze...Basin Prior 32 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=103, z=111, r=9856 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=18, CSF_MAX=53 , nb = 43571 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=22 , nb = -1034273316 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=16 , nb = 1091023919 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=19, CSF_MAX=51 , nb = 1080740452 LEFT_BRAIN CSF_MIN=0, CSF_intensity=18, CSF_MAX=57 , nb = 1080393174 OTHER CSF_MIN=7, CSF_intensity=21, CSF_MAX=71 , nb = 1075364742 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 53, 44, 34, 76 after analyzing : 37, 44, 44, 52 RIGHT_CER before analyzing : 22, 21, 21, 80 after analyzing : 21, 23, 25, 37 LEFT_CER before analyzing : 16, 21, 40, 84 after analyzing : 16, 33, 40, 45 RIGHT_BRAIN before analyzing : 51, 43, 34, 76 after analyzing : 36, 43, 43, 51 LEFT_BRAIN before analyzing : 57, 46, 36, 76 after analyzing : 39, 46, 46, 53 OTHER before analyzing : 71, 78, 80, 93 after analyzing : 71, 79, 80, 82 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...84 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 70.103, std = 9.713 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.81, sigma = 5.96 after rotation: sse = 3.81, sigma = 5.96 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.17, its var is 5.75 before Erosion-Dilatation 1.61% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...41 iterations mri_strip_skull: done peeling brain Brain Size = 1738897 voxels, voxel volume = 1.000 mm3 = 1738897 mmm3 = 1738.897 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 24.330243 mri_watershed stimesec 0.416149 mri_watershed ru_maxrss 860576 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 213634 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9688 mri_watershed ru_oublock 2800 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 2825 mri_watershed ru_nivcsw 243 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Feb 27 15:42:26 UTC 2020 /execute/freesurfer/mri mri_em_register -rusage /execute/freesurfer/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, 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=16.1 skull bounding box = (64, 34, 30) --> (193, 176, 202) using (107, 81, 116) as brain centroid... mean wm in atlas = 107, using box (91,64,95) --> (122, 98,137) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 6.9 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.478 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.297153 @ (-9.091, 9.091, -9.091) max log p = -4.118011 @ (4.545, 4.545, -4.545) max log p = -4.077608 @ (2.273, 6.818, 2.273) max log p = -4.064380 @ (-1.136, -1.136, 1.136) max log p = -4.050344 @ (-0.568, -0.568, 0.568) max log p = -4.050344 @ (0.000, 0.000, 0.000) Found translation: (-4.0, 18.7, -9.7): log p = -4.050 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.900, old_max_log_p =-4.050 (thresh=-4.0) 1.00000 0.00000 0.00000 -3.97727; 0.00000 1.03837 0.27823 -17.13304; 0.00000 -0.23941 0.89348 34.17162; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.900, old_max_log_p =-3.900 (thresh=-3.9) 1.00000 0.00000 0.00000 -3.97727; 0.00000 1.03837 0.27823 -17.13304; 0.00000 -0.23941 0.89348 34.17162; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.842, old_max_log_p =-3.900 (thresh=-3.9) 1.03675 0.01008 -0.02542 -7.23645; 0.00491 0.99522 0.20096 -3.01986; 0.02976 -0.18022 0.94259 15.44422; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.840, old_max_log_p =-3.842 (thresh=-3.8) 1.01736 0.03481 0.01254 -11.36098; -0.02859 1.00668 0.23574 -3.62107; -0.00427 -0.20891 0.91830 27.32730; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.824, old_max_log_p =-3.840 (thresh=-3.8) 1.01828 0.04487 0.00688 -10.93354; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.809, old_max_log_p =-3.824 (thresh=-3.8) 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.809, old_max_log_p =-3.809 (thresh=-3.8) 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.809 (old=-4.478) transform before final EM align: 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.1 tol 0.000000 final transform: 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1026.947385 mri_em_register stimesec 2.256066 mri_em_register ru_maxrss 603852 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 166555 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 537 mri_em_register ru_nivcsw 11634 registration took 4 minutes and 52 seconds. #-------------------------------------- #@# CA Normalize Thu Feb 27 15:47:17 UTC 2020 /execute/freesurfer/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.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 '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.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=16.1 skull bounding box = (64, 34, 30) --> (193, 176, 202) using (107, 81, 116) as brain centroid... mean wm in atlas = 107, using box (91,64,95) --> (122, 98,137) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 6.9 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 35, 27) --> (195, 149, 202) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 592 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 35, 26) --> (132, 145, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 311 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 125, 57) --> (176, 168, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 204 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 125, 54) --> (128, 164, 115) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 100 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 111, 95) --> (146, 180, 126) Brain_Stem: limiting intensities to 97.0 --> 132.0 0 of 72 (0.0%) samples deleted using 1279 total control points for intensity normalization... bias field = 0.970 +- 0.117 0 of 1277 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 35, 27) --> (195, 149, 202) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 587 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 35, 26) --> (132, 145, 202) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 141 of 339 (41.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 125, 57) --> (176, 168, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 22 of 293 (7.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 125, 54) --> (128, 164, 115) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 31 of 177 (17.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 111, 95) --> (146, 180, 126) Brain_Stem: limiting intensities to 95.0 --> 132.0 46 of 111 (41.4%) samples deleted using 1507 total control points for intensity normalization... bias field = 0.979 +- 0.082 0 of 1244 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 35, 27) --> (195, 149, 202) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 647 (0.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 35, 26) --> (132, 145, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 35 of 437 (8.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 125, 57) --> (176, 168, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 115 of 353 (32.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 125, 54) --> (128, 164, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 98 of 229 (42.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 111, 95) --> (146, 180, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 91 of 248 (36.7%) samples deleted using 1914 total control points for intensity normalization... bias field = 0.994 +- 0.070 0 of 1540 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 15 seconds. #-------------------------------------- #@# CA Reg Thu Feb 27 15:48:33 UTC 2020 /execute/freesurfer/mri mri_ca_register -rusage /execute/freesurfer/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.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 = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.99 (predicted orig area = 8.1) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.071, neg=0, invalid=762 0001: dt=320.325480, rms=0.935 (12.674%), neg=0, invalid=762 0002: dt=427.071090, rms=0.882 (5.710%), neg=0, invalid=762 0003: dt=196.637681, rms=0.866 (1.813%), neg=0, invalid=762 0004: dt=517.888000, rms=0.845 (2.443%), neg=0, invalid=762 0005: dt=221.952000, rms=0.838 (0.815%), neg=0, invalid=762 0006: dt=517.888000, rms=0.831 (0.857%), neg=0, invalid=762 0007: dt=168.080808, rms=0.825 (0.733%), neg=0, invalid=762 0008: dt=517.888000, rms=0.819 (0.647%), neg=0, invalid=762 0009: dt=221.952000, rms=0.816 (0.437%), neg=0, invalid=762 0010: dt=221.952000, rms=0.814 (0.252%), neg=0, invalid=762 0011: dt=443.904000, rms=0.810 (0.397%), neg=0, invalid=762 0012: dt=129.472000, rms=0.808 (0.259%), neg=0, invalid=762 0013: dt=4734.976000, rms=0.789 (2.408%), neg=0, invalid=762 0014: dt=221.952000, rms=0.786 (0.392%), neg=0, invalid=762 0015: dt=295.936000, rms=0.784 (0.231%), neg=0, invalid=762 0016: dt=295.936000, rms=0.783 (0.113%), neg=0, invalid=762 0017: dt=295.936000, rms=0.780 (0.385%), neg=0, invalid=762 0018: dt=295.936000, rms=0.779 (0.157%), neg=0, invalid=762 0019: dt=295.936000, rms=0.776 (0.397%), neg=0, invalid=762 0020: dt=295.936000, rms=0.774 (0.245%), neg=0, invalid=762 0021: dt=295.936000, rms=0.771 (0.317%), neg=0, invalid=762 0022: dt=295.936000, rms=0.768 (0.435%), neg=0, invalid=762 0023: dt=295.936000, rms=0.764 (0.448%), neg=0, invalid=762 0024: dt=295.936000, rms=0.761 (0.451%), neg=0, invalid=762 0025: dt=295.936000, rms=0.759 (0.295%), neg=0, invalid=762 0026: dt=295.936000, rms=0.755 (0.433%), neg=0, invalid=762 0027: dt=295.936000, rms=0.753 (0.329%), neg=0, invalid=762 0028: dt=295.936000, rms=0.751 (0.201%), neg=0, invalid=762 0029: dt=295.936000, rms=0.749 (0.323%), neg=0, invalid=762 0030: dt=295.936000, rms=0.747 (0.259%), neg=0, invalid=762 0031: dt=295.936000, rms=0.746 (0.205%), neg=0, invalid=762 0032: dt=295.936000, rms=0.744 (0.173%), neg=0, invalid=762 0033: dt=295.936000, rms=0.743 (0.215%), neg=0, invalid=762 0034: dt=295.936000, rms=0.741 (0.184%), neg=0, invalid=762 0035: dt=295.936000, rms=0.741 (0.099%), neg=0, invalid=762 0036: dt=295.936000, rms=0.739 (0.191%), neg=0, invalid=762 0037: dt=295.936000, rms=0.738 (0.181%), neg=0, invalid=762 0038: dt=295.936000, rms=0.737 (0.097%), neg=0, invalid=762 0039: dt=295.936000, rms=0.736 (0.113%), neg=0, invalid=762 0040: dt=295.936000, rms=0.736 (0.076%), neg=0, invalid=762 0041: dt=129.472000, rms=0.736 (0.030%), neg=0, invalid=762 0042: dt=129.472000, rms=0.735 (0.006%), neg=0, invalid=762 0043: dt=129.472000, rms=0.735 (0.010%), neg=0, invalid=762 0044: dt=129.472000, rms=0.735 (0.012%), neg=0, invalid=762 0045: dt=129.472000, rms=0.735 (0.011%), neg=0, invalid=762 0046: dt=129.472000, rms=0.735 (0.015%), neg=0, invalid=762 0047: dt=129.472000, rms=0.735 (0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.736, neg=0, invalid=762 0048: dt=129.472000, rms=0.735 (0.220%), neg=0, invalid=762 0049: dt=443.904000, rms=0.734 (0.084%), neg=0, invalid=762 0050: dt=443.904000, rms=0.733 (0.107%), neg=0, invalid=762 0051: dt=443.904000, rms=0.733 (0.038%), neg=0, invalid=762 0052: dt=443.904000, rms=0.733 (-0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.747, neg=0, invalid=762 0053: dt=187.076923, rms=0.738 (1.279%), neg=0, invalid=762 0054: dt=169.902813, rms=0.727 (1.422%), neg=0, invalid=762 0055: dt=82.428016, rms=0.721 (0.889%), neg=0, invalid=762 0056: dt=155.371069, rms=0.717 (0.510%), neg=0, invalid=762 0057: dt=83.027027, rms=0.712 (0.627%), neg=0, invalid=762 0058: dt=103.680000, rms=0.710 (0.331%), neg=0, invalid=762 0059: dt=103.680000, rms=0.707 (0.404%), neg=0, invalid=762 0060: dt=86.119816, rms=0.705 (0.256%), neg=0, invalid=762 0061: dt=145.152000, rms=0.703 (0.320%), neg=0, invalid=762 0062: dt=62.208000, rms=0.701 (0.246%), neg=0, invalid=762 0063: dt=62.208000, rms=0.700 (0.161%), neg=0, invalid=762 0064: dt=62.208000, rms=0.699 (0.249%), neg=0, invalid=762 0065: dt=62.208000, rms=0.696 (0.326%), neg=0, invalid=762 0066: dt=62.208000, rms=0.694 (0.367%), neg=0, invalid=762 0067: dt=62.208000, rms=0.691 (0.394%), neg=0, invalid=762 0068: dt=62.208000, rms=0.688 (0.394%), neg=0, invalid=762 0069: dt=62.208000, rms=0.686 (0.367%), neg=0, invalid=762 0070: dt=62.208000, rms=0.683 (0.345%), neg=0, invalid=762 0071: dt=62.208000, rms=0.681 (0.308%), neg=0, invalid=762 0072: dt=62.208000, rms=0.679 (0.282%), neg=0, invalid=762 0073: dt=62.208000, rms=0.678 (0.251%), neg=0, invalid=762 0074: dt=62.208000, rms=0.676 (0.224%), neg=0, invalid=762 0075: dt=62.208000, rms=0.675 (0.206%), neg=0, invalid=762 0076: dt=62.208000, rms=0.674 (0.187%), neg=0, invalid=762 0077: dt=62.208000, rms=0.672 (0.173%), neg=0, invalid=762 0078: dt=62.208000, rms=0.671 (0.156%), neg=0, invalid=762 0079: dt=62.208000, rms=0.670 (0.143%), neg=0, invalid=762 0080: dt=62.208000, rms=0.669 (0.144%), neg=0, invalid=762 0081: dt=62.208000, rms=0.668 (0.134%), neg=0, invalid=762 0082: dt=62.208000, rms=0.668 (0.143%), neg=0, invalid=762 0083: dt=62.208000, rms=0.667 (0.131%), neg=0, invalid=762 0084: dt=62.208000, rms=0.666 (0.117%), neg=0, invalid=762 0085: dt=62.208000, rms=0.665 (0.109%), neg=0, invalid=762 0086: dt=145.152000, rms=0.665 (0.025%), neg=0, invalid=762 0087: dt=145.152000, rms=0.665 (0.004%), neg=0, invalid=762 0088: dt=145.152000, rms=0.665 (0.031%), neg=0, invalid=762 0089: dt=145.152000, rms=0.664 (0.059%), neg=0, invalid=762 0090: dt=145.152000, rms=0.664 (0.076%), neg=0, invalid=762 0091: dt=145.152000, rms=0.664 (0.031%), neg=0, invalid=762 0092: dt=145.152000, rms=0.663 (0.098%), neg=0, invalid=762 0093: dt=145.152000, rms=0.662 (0.073%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0094: dt=36.288000, rms=0.662 (0.233%), neg=0, invalid=762 0095: dt=36.288000, rms=0.662 (0.020%), neg=0, invalid=762 0096: dt=36.288000, rms=0.662 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.703, neg=0, invalid=762 0097: dt=0.000000, rms=0.702 (0.154%), neg=0, invalid=762 0098: dt=0.000000, rms=0.702 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=762 0099: dt=0.000000, rms=0.702 (0.154%), neg=0, invalid=762 0100: dt=0.000000, rms=0.702 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.820, neg=0, invalid=762 0101: dt=5.855769, rms=0.792 (3.432%), neg=0, invalid=762 0102: dt=3.274725, rms=0.790 (0.224%), neg=0, invalid=762 0103: dt=3.274725, rms=0.790 (-0.087%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.791, neg=0, invalid=762 0104: dt=0.000000, rms=0.790 (0.101%), neg=0, invalid=762 0105: dt=0.000000, rms=0.790 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.909, neg=0, invalid=762 0106: dt=1.536000, rms=0.903 (0.678%), neg=0, invalid=762 0107: dt=2.393782, rms=0.893 (1.101%), neg=0, invalid=762 0108: dt=0.448000, rms=0.892 (0.080%), neg=0, invalid=762 0109: dt=0.448000, rms=0.892 (0.036%), neg=0, invalid=762 0110: dt=0.448000, rms=0.891 (0.024%), neg=0, invalid=762 0111: dt=0.448000, rms=0.891 (0.014%), neg=0, invalid=762 0112: dt=1.792000, rms=0.889 (0.317%), neg=0, invalid=762 0113: dt=0.000000, rms=0.889 (0.000%), neg=0, invalid=762 0114: dt=0.100000, rms=0.889 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.889, neg=0, invalid=762 0115: dt=0.256000, rms=0.888 (0.083%), neg=0, invalid=762 0116: dt=0.028000, rms=0.888 (0.000%), neg=0, invalid=762 0117: dt=0.028000, rms=0.888 (0.000%), neg=0, invalid=762 0118: dt=0.028000, rms=0.888 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.786, neg=0, invalid=762 0119: dt=0.971954, rms=0.762 (3.088%), neg=0, invalid=762 0120: dt=0.096000, rms=0.760 (0.168%), neg=0, invalid=762 0121: dt=0.096000, rms=0.760 (-0.075%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.761, neg=0, invalid=762 0122: dt=0.028000, rms=0.760 (0.114%), neg=0, invalid=762 0123: dt=0.016000, rms=0.760 (0.003%), neg=0, invalid=762 0124: dt=0.016000, rms=0.760 (-0.004%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.13926 (26) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (3471 voxels, overlap=0.538) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (3471 voxels, peak = 28), gca=27.5 gca peak = 0.15565 (16) mri peak = 0.13431 (26) Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (2256 voxels, overlap=0.323) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2256 voxels, peak = 26), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.06166 (110) Right_Pallidum (52): linear fit = 1.16 x + 0.0 (1116 voxels, overlap=0.038) Right_Pallidum (52): linear fit = 1.16 x + 0.0 (1116 voxels, peak = 112), gca=111.8 gca peak = 0.20183 (93) mri peak = 0.08070 (112) Left_Pallidum (13): linear fit = 1.18 x + 0.0 (1136 voxels, overlap=0.032) Left_Pallidum (13): linear fit = 1.18 x + 0.0 (1136 voxels, peak = 110), gca=110.2 gca peak = 0.21683 (55) mri peak = 0.08765 (73) Right_Hippocampus (53): linear fit = 1.28 x + 0.0 (697 voxels, overlap=0.009) Right_Hippocampus (53): linear fit = 1.28 x + 0.0 (697 voxels, peak = 71), gca=70.7 gca peak = 0.30730 (58) mri peak = 0.09750 (71) Left_Hippocampus (17): linear fit = 1.24 x + 0.0 (932 voxels, overlap=0.013) Left_Hippocampus (17): linear fit = 1.24 x + 0.0 (932 voxels, peak = 72), gca=71.6 gca peak = 0.11430 (101) mri peak = 0.04941 (103) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (64932 voxels, overlap=0.977) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (64932 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.05911 (104) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (67071 voxels, overlap=0.978) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (67071 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03132 (72) Left_Cerebral_Cortex (3): linear fit = 1.23 x + 0.0 (25456 voxels, overlap=0.010) Left_Cerebral_Cortex (3): linear fit = 1.23 x + 0.0 (25456 voxels, peak = 72), gca=72.3 gca peak = 0.15082 (58) mri peak = 0.03293 (70) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (28017 voxels, overlap=0.007) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (28017 voxels, peak = 71), gca=71.1 gca peak = 0.14161 (67) mri peak = 0.17074 (86) Right_Caudate (50): linear fit = 1.30 x + 0.0 (1220 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.30 x + 0.0 (1220 voxels, peak = 87), gca=87.4 gca peak = 0.15243 (71) mri peak = 0.08743 (87) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1013 voxels, overlap=0.020) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1013 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.02966 (60) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27975 voxels, overlap=0.548) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27975 voxels, peak = 60), gca=59.6 gca peak = 0.13252 (56) mri peak = 0.03139 (56) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (32180 voxels, overlap=0.797) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (32180 voxels, peak = 59), gca=58.5 gca peak = 0.18181 (84) mri peak = 0.06494 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (11716 voxels, overlap=0.527) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (11716 voxels, peak = 89), gca=89.5 gca peak = 0.20573 (83) mri peak = 0.06184 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (10260 voxels, overlap=0.749) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (10260 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.12098 (73) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (336 voxels, overlap=0.041) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (336 voxels, peak = 72), gca=71.5 gca peak = 0.39313 (56) mri peak = 0.08748 (70) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (526 voxels, overlap=0.014) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (526 voxels, peak = 69), gca=68.6 gca peak = 0.14181 (85) mri peak = 0.05902 (97) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (4987 voxels, overlap=0.242) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (4987 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.06949 (100) Right_Thalamus_Proper (49): linear fit = 1.18 x + 0.0 (3746 voxels, overlap=0.104) Right_Thalamus_Proper (49): linear fit = 1.18 x + 0.0 (3746 voxels, peak = 98), gca=98.4 gca peak = 0.13399 (79) mri peak = 0.06690 (90) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2772 voxels, overlap=0.067) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2772 voxels, peak = 91), gca=91.2 gca peak = 0.14159 (79) mri peak = 0.08304 (88) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2858 voxels, overlap=0.119) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2858 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.06835 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13728 voxels, overlap=0.403) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13728 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.10236 (104) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (1640 voxels, overlap=0.015) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (1640 voxels, peak = 102), gca=101.9 gca peak = 0.12801 (89) mri peak = 0.09072 (108) Left_VentralDC (28): linear fit = 1.21 x + 0.0 (1848 voxels, overlap=0.013) Left_VentralDC (28): linear fit = 1.21 x + 0.0 (1848 voxels, peak = 107), gca=107.2 gca peak = 0.20494 (23) mri peak = 0.15517 (31) Third_Ventricle (14): linear fit = 1.28 x + 0.0 (171 voxels, overlap=0.316) Third_Ventricle (14): linear fit = 1.28 x + 0.0 (171 voxels, peak = 30), gca=29.6 gca peak = 0.15061 (21) mri peak = 0.10266 (23) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (1058 voxels, overlap=0.715) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (1058 voxels, peak = 26), gca=25.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.24 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.34 x + 0.0 Left_Pallidum too bright - rescaling by 0.925 (from 1.185) to 101.9 (was 110.2) Right_Pallidum too bright - rescaling by 0.911 (from 1.165) to 101.9 (was 111.8) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.811, neg=0, invalid=762 0125: dt=110.976000, rms=0.797 (1.812%), neg=0, invalid=762 0126: dt=295.936000, rms=0.788 (1.087%), neg=0, invalid=762 0127: dt=443.904000, rms=0.779 (1.114%), neg=0, invalid=762 0128: dt=92.480000, rms=0.778 (0.181%), neg=0, invalid=762 0129: dt=295.936000, rms=0.777 (0.130%), neg=0, invalid=762 0130: dt=517.888000, rms=0.773 (0.547%), neg=0, invalid=762 0131: dt=92.480000, rms=0.772 (0.091%), neg=0, invalid=762 0132: dt=369.920000, rms=0.771 (0.087%), neg=0, invalid=762 0133: dt=369.920000, rms=0.768 (0.382%), neg=0, invalid=762 0134: dt=92.480000, rms=0.768 (0.075%), neg=0, invalid=762 0135: dt=369.920000, rms=0.767 (0.080%), neg=0, invalid=762 0136: dt=369.920000, rms=0.765 (0.319%), neg=0, invalid=762 0137: dt=92.480000, rms=0.764 (0.069%), neg=0, invalid=762 0138: dt=295.936000, rms=0.764 (0.066%), neg=0, invalid=762 0139: dt=443.904000, rms=0.762 (0.268%), neg=0, invalid=762 0140: dt=92.480000, rms=0.761 (0.073%), neg=0, invalid=762 0141: dt=369.920000, rms=0.760 (0.079%), neg=0, invalid=762 0142: dt=295.936000, rms=0.759 (0.199%), neg=0, invalid=762 0143: dt=129.472000, rms=0.759 (0.055%), neg=0, invalid=762 0144: dt=2071.552000, rms=0.754 (0.607%), neg=0, invalid=762 0145: dt=110.976000, rms=0.753 (0.185%), neg=0, invalid=762 0146: dt=2071.552000, rms=0.749 (0.475%), neg=0, invalid=762 0147: dt=110.976000, rms=0.748 (0.157%), neg=0, invalid=762 0148: dt=221.952000, rms=0.747 (0.060%), neg=0, invalid=762 0149: dt=1183.744000, rms=0.745 (0.287%), neg=0, invalid=762 0150: dt=92.480000, rms=0.744 (0.111%), neg=0, invalid=762 0151: dt=73.984000, rms=0.744 (0.010%), neg=0, invalid=762 0152: dt=73.984000, rms=0.744 (0.005%), neg=0, invalid=762 0153: dt=73.984000, rms=0.744 (0.012%), neg=0, invalid=762 0154: dt=73.984000, rms=0.744 (0.023%), neg=0, invalid=762 0155: dt=73.984000, rms=0.744 (0.051%), neg=0, invalid=762 0156: dt=73.984000, rms=0.743 (0.073%), neg=0, invalid=762 0157: dt=73.984000, rms=0.742 (0.087%), neg=0, invalid=762 0158: dt=73.984000, rms=0.742 (0.092%), neg=0, invalid=762 0159: dt=73.984000, rms=0.741 (0.087%), neg=0, invalid=762 0160: dt=73.984000, rms=0.740 (0.088%), neg=0, invalid=762 0161: dt=73.984000, rms=0.740 (0.087%), neg=0, invalid=762 0162: dt=73.984000, rms=0.739 (0.093%), neg=0, invalid=762 0163: dt=73.984000, rms=0.738 (0.096%), neg=0, invalid=762 0164: dt=73.984000, rms=0.738 (0.105%), neg=0, invalid=762 0165: dt=73.984000, rms=0.737 (0.107%), neg=0, invalid=762 0166: dt=73.984000, rms=0.736 (0.103%), neg=0, invalid=762 0167: dt=73.984000, rms=0.735 (0.101%), neg=0, invalid=762 0168: dt=73.984000, rms=0.735 (0.091%), neg=0, invalid=762 0169: dt=73.984000, rms=0.734 (0.090%), neg=0, invalid=762 0170: dt=73.984000, rms=0.733 (0.089%), neg=0, invalid=762 0171: dt=73.984000, rms=0.733 (0.087%), neg=0, invalid=762 0172: dt=73.984000, rms=0.732 (0.084%), neg=0, invalid=762 0173: dt=73.984000, rms=0.731 (0.084%), neg=0, invalid=762 0174: dt=73.984000, rms=0.731 (0.083%), neg=0, invalid=762 0175: dt=73.984000, rms=0.730 (0.080%), neg=0, invalid=762 0176: dt=73.984000, rms=0.730 (0.073%), neg=0, invalid=762 0177: dt=73.984000, rms=0.729 (0.066%), neg=0, invalid=762 0178: dt=73.984000, rms=0.729 (0.060%), neg=0, invalid=762 0179: dt=73.984000, rms=0.728 (0.060%), neg=0, invalid=762 0180: dt=73.984000, rms=0.728 (0.054%), neg=0, invalid=762 0181: dt=73.984000, rms=0.728 (0.059%), neg=0, invalid=762 0182: dt=73.984000, rms=0.727 (0.060%), neg=0, invalid=762 0183: dt=73.984000, rms=0.727 (0.055%), neg=0, invalid=762 0184: dt=73.984000, rms=0.726 (0.047%), neg=0, invalid=762 0185: dt=73.984000, rms=0.726 (0.045%), neg=0, invalid=762 0186: dt=73.984000, rms=0.726 (0.043%), neg=0, invalid=762 0187: dt=73.984000, rms=0.725 (0.042%), neg=0, invalid=762 0188: dt=73.984000, rms=0.725 (0.046%), neg=0, invalid=762 0189: dt=73.984000, rms=0.725 (0.045%), neg=0, invalid=762 0190: dt=73.984000, rms=0.724 (0.044%), neg=0, invalid=762 0191: dt=73.984000, rms=0.724 (0.038%), neg=0, invalid=762 0192: dt=73.984000, rms=0.724 (0.040%), neg=0, invalid=762 0193: dt=73.984000, rms=0.724 (0.043%), neg=0, invalid=762 0194: dt=73.984000, rms=0.723 (0.043%), neg=0, invalid=762 0195: dt=73.984000, rms=0.723 (0.040%), neg=0, invalid=762 0196: dt=73.984000, rms=0.723 (0.036%), neg=0, invalid=762 0197: dt=73.984000, rms=0.723 (0.032%), neg=0, invalid=762 0198: dt=73.984000, rms=0.722 (0.030%), neg=0, invalid=762 0199: dt=73.984000, rms=0.722 (0.033%), neg=0, invalid=762 0200: dt=73.984000, rms=0.722 (0.035%), neg=0, invalid=762 0201: dt=73.984000, rms=0.722 (0.033%), neg=0, invalid=762 0202: dt=73.984000, rms=0.722 (0.003%), neg=0, invalid=762 0203: dt=73.984000, rms=0.722 (0.006%), neg=0, invalid=762 0204: dt=73.984000, rms=0.721 (0.005%), neg=0, invalid=762 0205: dt=1.445000, rms=0.721 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0206: dt=92.480000, rms=0.721 (0.230%), neg=0, invalid=762 0207: dt=129.472000, rms=0.721 (0.024%), neg=0, invalid=762 0208: dt=129.472000, rms=0.721 (0.025%), neg=0, invalid=762 0209: dt=129.472000, rms=0.721 (0.026%), neg=0, invalid=762 0210: dt=129.472000, rms=0.720 (0.028%), neg=0, invalid=762 0211: dt=129.472000, rms=0.720 (0.046%), neg=0, invalid=762 0212: dt=129.472000, rms=0.720 (0.034%), neg=0, invalid=762 0213: dt=129.472000, rms=0.720 (0.020%), neg=0, invalid=762 0214: dt=129.472000, rms=0.719 (0.037%), neg=0, invalid=762 0215: dt=129.472000, rms=0.719 (0.031%), neg=0, invalid=762 0216: dt=129.472000, rms=0.719 (0.010%), neg=0, invalid=762 0217: dt=129.472000, rms=0.719 (0.005%), neg=0, invalid=762 0218: dt=517.888000, rms=0.719 (0.025%), neg=0, invalid=762 0219: dt=221.952000, rms=0.719 (0.018%), neg=0, invalid=762 0220: dt=221.952000, rms=0.719 (0.001%), neg=0, invalid=762 0221: dt=221.952000, rms=0.719 (0.005%), neg=0, invalid=762 0222: dt=221.952000, rms=0.719 (0.038%), neg=0, invalid=762 0223: dt=221.952000, rms=0.718 (0.030%), neg=0, invalid=762 0224: dt=221.952000, rms=0.718 (0.028%), neg=0, invalid=762 0225: dt=221.952000, rms=0.718 (-0.000%), neg=0, invalid=762 0226: dt=0.005645, rms=0.718 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.721, neg=0, invalid=762 0227: dt=36.288000, rms=0.716 (0.758%), neg=0, invalid=762 0228: dt=36.288000, rms=0.712 (0.452%), neg=0, invalid=762 0229: dt=2.268000, rms=0.712 (0.026%), neg=0, invalid=762 0230: dt=1.134000, rms=0.712 (0.012%), neg=0, invalid=762 0231: dt=0.567000, rms=0.712 (0.006%), neg=0, invalid=762 0232: dt=0.283500, rms=0.712 (0.003%), neg=0, invalid=762 0233: dt=0.141750, rms=0.712 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.713, neg=0, invalid=762 0234: dt=145.152000, rms=0.705 (1.101%), neg=0, invalid=762 0235: dt=145.152000, rms=0.696 (1.293%), neg=0, invalid=762 0236: dt=124.416000, rms=0.694 (0.339%), neg=0, invalid=762 0237: dt=181.735849, rms=0.687 (0.950%), neg=0, invalid=762 0238: dt=75.707317, rms=0.685 (0.361%), neg=0, invalid=762 0239: dt=145.152000, rms=0.681 (0.605%), neg=0, invalid=762 0240: dt=72.648649, rms=0.679 (0.229%), neg=0, invalid=762 0241: dt=248.832000, rms=0.675 (0.619%), neg=0, invalid=762 0242: dt=36.288000, rms=0.673 (0.304%), neg=0, invalid=762 0243: dt=77.298701, rms=0.672 (0.163%), neg=0, invalid=762 0244: dt=145.152000, rms=0.669 (0.400%), neg=0, invalid=762 0245: dt=64.328205, rms=0.668 (0.126%), neg=0, invalid=762 0246: dt=103.680000, rms=0.666 (0.271%), neg=0, invalid=762 0247: dt=2.268000, rms=0.666 (0.005%), neg=0, invalid=762 0248: dt=2.268000, rms=0.666 (0.005%), neg=0, invalid=762 0249: dt=1.134000, rms=0.666 (0.002%), neg=0, invalid=762 0250: dt=0.283500, rms=0.666 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.674, neg=0, invalid=762 0251: dt=38.400000, rms=0.647 (4.038%), neg=0, invalid=762 0252: dt=8.000000, rms=0.643 (0.549%), neg=0, invalid=762 0253: dt=2.000000, rms=0.642 (0.127%), neg=0, invalid=762 0254: dt=0.125000, rms=0.642 (0.008%), neg=0, invalid=762 0255: dt=0.015625, rms=0.642 (0.001%), neg=0, invalid=762 0256: dt=0.007812, rms=0.642 (0.000%), neg=0, invalid=762 0257: dt=0.000977, rms=0.642 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=762 0258: dt=32.000000, rms=0.634 (1.591%), neg=0, invalid=762 0259: dt=44.800000, rms=0.623 (1.715%), neg=0, invalid=762 0260: dt=32.000000, rms=0.617 (0.969%), neg=0, invalid=762 0261: dt=44.800000, rms=0.611 (0.997%), neg=0, invalid=762 0262: dt=11.200000, rms=0.609 (0.292%), neg=0, invalid=762 0263: dt=32.000000, rms=0.605 (0.688%), neg=0, invalid=762 0264: dt=11.200000, rms=0.604 (0.164%), neg=0, invalid=762 0265: dt=11.200000, rms=0.603 (0.172%), neg=0, invalid=762 0266: dt=11.200000, rms=0.601 (0.175%), neg=0, invalid=762 0267: dt=2.800000, rms=0.601 (0.041%), neg=0, invalid=762 0268: dt=0.700000, rms=0.601 (0.010%), neg=0, invalid=762 0269: dt=0.087500, rms=0.601 (0.001%), neg=0, invalid=762 0270: dt=0.043750, rms=0.601 (0.001%), neg=0, invalid=762 0271: dt=0.009375, rms=0.601 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.625, neg=0, invalid=762 0272: dt=4.032000, rms=0.620 (0.734%), neg=0, invalid=762 0273: dt=1.008000, rms=0.620 (0.120%), neg=0, invalid=762 0274: dt=1.008000, rms=0.619 (0.117%), neg=0, invalid=762 0275: dt=1.008000, rms=0.618 (0.111%), neg=0, invalid=762 0276: dt=0.063000, rms=0.618 (0.007%), neg=0, invalid=762 0277: dt=0.031500, rms=0.618 (0.003%), neg=0, invalid=762 0278: dt=0.015750, rms=0.618 (0.002%), neg=0, invalid=762 0279: dt=0.007875, rms=0.618 (0.001%), neg=0, invalid=762 0280: dt=0.000984, rms=0.618 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=762 0281: dt=4.032000, rms=0.617 (0.362%), neg=0, invalid=762 0282: dt=0.003938, rms=0.617 (0.001%), neg=0, invalid=762 0283: dt=0.003938, rms=0.617 (0.000%), neg=0, invalid=762 0284: dt=0.001969, rms=0.617 (0.000%), neg=0, invalid=762 0285: dt=0.000123, rms=0.617 (0.000%), neg=0, invalid=762 0286: dt=0.000000, rms=0.617 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.660, neg=0, invalid=762 0287: dt=0.448000, rms=0.659 (0.185%), neg=0, invalid=762 0288: dt=0.384000, rms=0.659 (0.008%), neg=0, invalid=762 0289: dt=0.384000, rms=0.659 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.660, neg=0, invalid=762 0290: dt=1.024000, rms=0.658 (0.221%), neg=0, invalid=762 0291: dt=0.384000, rms=0.658 (-0.001%), neg=0, invalid=762 0292: dt=0.384000, rms=0.658 (0.004%), neg=0, invalid=762 0293: dt=0.384000, rms=0.658 (-0.017%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.596, neg=0, invalid=762 0294: dt=0.448000, rms=0.578 (3.046%), neg=0, invalid=762 0295: dt=0.448000, rms=0.572 (1.000%), neg=0, invalid=762 0296: dt=0.320000, rms=0.570 (0.405%), neg=0, invalid=762 0297: dt=0.320000, rms=0.568 (0.304%), neg=0, invalid=762 0298: dt=0.112000, rms=0.568 (0.085%), neg=0, invalid=762 0299: dt=0.384000, rms=0.566 (0.273%), neg=0, invalid=762 0300: dt=0.112000, rms=0.566 (0.058%), neg=0, invalid=762 0301: dt=0.448000, rms=0.565 (0.231%), neg=0, invalid=762 0302: dt=0.112000, rms=0.564 (0.048%), neg=0, invalid=762 0303: dt=0.112000, rms=0.564 (0.044%), neg=0, invalid=762 0304: dt=0.112000, rms=0.564 (0.079%), neg=0, invalid=762 0305: dt=0.112000, rms=0.563 (0.104%), neg=0, invalid=762 0306: dt=0.112000, rms=0.562 (0.127%), neg=0, invalid=762 0307: dt=0.112000, rms=0.562 (0.135%), neg=0, invalid=762 0308: dt=0.112000, rms=0.561 (0.148%), neg=0, invalid=762 0309: dt=0.112000, rms=0.560 (0.140%), neg=0, invalid=762 0310: dt=0.112000, rms=0.559 (0.131%), neg=0, invalid=762 0311: dt=0.112000, rms=0.559 (0.119%), neg=0, invalid=762 0312: dt=0.112000, rms=0.558 (0.102%), neg=0, invalid=762 0313: dt=0.112000, rms=0.557 (0.086%), neg=0, invalid=762 0314: dt=0.112000, rms=0.557 (0.073%), neg=0, invalid=762 0315: dt=0.112000, rms=0.557 (0.055%), neg=0, invalid=762 0316: dt=0.112000, rms=0.557 (0.041%), neg=0, invalid=762 0317: dt=0.112000, rms=0.556 (0.031%), neg=0, invalid=762 0318: dt=0.112000, rms=0.556 (0.018%), neg=0, invalid=762 0319: dt=0.112000, rms=0.556 (0.009%), neg=0, invalid=762 0320: dt=0.000000, rms=0.556 (0.001%), neg=0, invalid=762 0321: dt=0.050000, rms=0.556 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=762 0322: dt=0.320000, rms=0.553 (0.783%), neg=0, invalid=762 0323: dt=0.320000, rms=0.552 (0.184%), neg=0, invalid=762 0324: dt=0.112000, rms=0.552 (0.023%), neg=0, invalid=762 0325: dt=0.112000, rms=0.552 (0.011%), neg=0, invalid=762 0326: dt=0.112000, rms=0.552 (0.017%), neg=0, invalid=762 0327: dt=0.112000, rms=0.552 (0.012%), neg=0, invalid=762 0328: dt=0.112000, rms=0.552 (0.001%), neg=0, invalid=762 0329: dt=0.000000, rms=0.552 (0.001%), neg=0, invalid=762 0330: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.549, neg=0, invalid=762 0331: dt=32.368000, rms=0.548 (0.231%), neg=0, invalid=762 0332: dt=23.120000, rms=0.548 (0.001%), neg=0, invalid=762 0333: dt=23.120000, rms=0.548 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.549, neg=0, invalid=762 0334: dt=32.368000, rms=0.548 (0.208%), neg=0, invalid=762 0335: dt=32.368000, rms=0.548 (0.006%), neg=0, invalid=762 0336: dt=32.368000, rms=0.548 (0.004%), neg=0, invalid=762 0337: dt=32.368000, rms=0.548 (0.003%), neg=0, invalid=762 0338: dt=32.368000, rms=0.548 (0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.549, neg=0, invalid=762 0339: dt=36.288000, rms=0.547 (0.438%), neg=0, invalid=762 0340: dt=82.944000, rms=0.546 (0.143%), neg=0, invalid=762 0341: dt=82.944000, rms=0.545 (0.164%), neg=0, invalid=762 0342: dt=82.944000, rms=0.544 (0.137%), neg=0, invalid=762 0343: dt=82.944000, rms=0.544 (0.100%), neg=0, invalid=762 0344: dt=82.944000, rms=0.543 (0.035%), neg=0, invalid=762 0345: dt=145.152000, rms=0.543 (0.140%), neg=0, invalid=762 0346: dt=62.208000, rms=0.542 (0.093%), neg=0, invalid=762 0347: dt=62.208000, rms=0.542 (0.036%), neg=0, invalid=762 0348: dt=62.208000, rms=0.542 (0.066%), neg=0, invalid=762 0349: dt=62.208000, rms=0.541 (0.065%), neg=0, invalid=762 0350: dt=62.208000, rms=0.541 (0.096%), neg=0, invalid=762 0351: dt=62.208000, rms=0.540 (0.050%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0352: dt=36.288000, rms=0.540 (0.360%), neg=0, invalid=762 0353: dt=124.416000, rms=0.539 (0.172%), neg=0, invalid=762 0354: dt=124.416000, rms=0.538 (0.131%), neg=0, invalid=762 0355: dt=124.416000, rms=0.538 (0.098%), neg=0, invalid=762 0356: dt=124.416000, rms=0.538 (-0.119%), neg=0, invalid=762 0357: dt=31.104000, rms=0.537 (0.156%), neg=0, invalid=762 0358: dt=36.288000, rms=0.537 (0.038%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 iter 0, gcam->neg = 110 after 22 iterations, nbhd size=1, neg = 0 0359: dt=80.000000, rms=0.529 (1.657%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0360: dt=20.711510, rms=0.527 (0.386%), neg=0, invalid=762 iter 0, gcam->neg = 467 after 22 iterations, nbhd size=1, neg = 0 0361: dt=57.086420, rms=0.524 (0.643%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 13 iterations, nbhd size=1, neg = 0 0362: dt=23.485380, rms=0.523 (0.168%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 10 iterations, nbhd size=1, neg = 0 0363: dt=23.485380, rms=0.522 (0.260%), neg=0, invalid=762 iter 0, gcam->neg = 32 after 20 iterations, nbhd size=1, neg = 0 0364: dt=23.485380, rms=0.520 (0.277%), neg=0, invalid=762 iter 0, gcam->neg = 49 after 23 iterations, nbhd size=1, neg = 0 0365: dt=23.485380, rms=0.519 (0.250%), neg=0, invalid=762 iter 0, gcam->neg = 61 after 23 iterations, nbhd size=1, neg = 0 0366: dt=23.485380, rms=0.518 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 110 after 29 iterations, nbhd size=1, neg = 0 0367: dt=23.485380, rms=0.517 (0.240%), neg=0, invalid=762 iter 0, gcam->neg = 184 after 36 iterations, nbhd size=1, neg = 0 0368: dt=23.485380, rms=0.516 (0.246%), neg=0, invalid=762 iter 0, gcam->neg = 259 after 29 iterations, nbhd size=1, neg = 0 0369: dt=23.485380, rms=0.514 (0.240%), neg=0, invalid=762 iter 0, gcam->neg = 314 after 31 iterations, nbhd size=1, neg = 0 0370: dt=23.485380, rms=0.513 (0.247%), neg=0, invalid=762 iter 0, gcam->neg = 381 after 24 iterations, nbhd size=1, neg = 0 0371: dt=23.485380, rms=0.512 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 481 after 27 iterations, nbhd size=1, neg = 0 0372: dt=23.485380, rms=0.512 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 473 after 40 iterations, nbhd size=1, neg = 0 0373: dt=23.485380, rms=0.512 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 387 after 27 iterations, nbhd size=1, neg = 0 0374: dt=23.485380, rms=0.510 (0.313%), neg=0, invalid=762 iter 0, gcam->neg = 471 after 27 iterations, nbhd size=1, neg = 0 0375: dt=23.485380, rms=0.508 (0.425%), neg=0, invalid=762 iter 0, gcam->neg = 590 after 36 iterations, nbhd size=1, neg = 0 0376: dt=23.485380, rms=0.507 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 727 after 31 iterations, nbhd size=1, neg = 0 0377: dt=23.485380, rms=0.506 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 705 after 28 iterations, nbhd size=1, neg = 0 0378: dt=23.485380, rms=0.506 (-0.049%), neg=0, invalid=762 iter 0, gcam->neg = 61 after 20 iterations, nbhd size=1, neg = 0 0379: dt=32.000000, rms=0.506 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 62 after 28 iterations, nbhd size=1, neg = 0 0380: dt=44.800000, rms=0.505 (0.061%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=762 iter 0, gcam->neg = 18 after 16 iterations, nbhd size=1, neg = 0 0381: dt=32.000000, rms=0.504 (0.513%), neg=0, invalid=762 iter 0, gcam->neg = 31 after 24 iterations, nbhd size=1, neg = 0 0382: dt=44.800000, rms=0.503 (0.198%), neg=0, invalid=762 iter 0, gcam->neg = 47 after 16 iterations, nbhd size=1, neg = 0 0383: dt=44.800000, rms=0.503 (-0.048%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 iter 0, gcam->neg = 12 after 13 iterations, nbhd size=1, neg = 0 0384: dt=5.073171, rms=0.516 (0.399%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 12 iterations, nbhd size=1, neg = 0 0385: dt=4.909091, rms=0.516 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 14 iterations, nbhd size=1, neg = 0 0386: dt=4.909091, rms=0.515 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 21 iterations, nbhd size=1, neg = 0 0387: dt=4.909091, rms=0.515 (-0.044%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 iter 0, gcam->neg = 41 after 14 iterations, nbhd size=1, neg = 0 0388: dt=7.714286, rms=0.515 (0.320%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0389: dt=7.600000, rms=0.514 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 50 after 20 iterations, nbhd size=1, neg = 0 0390: dt=7.600000, rms=0.514 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 100 after 13 iterations, nbhd size=1, neg = 0 0391: dt=7.600000, rms=0.514 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 95 after 20 iterations, nbhd size=1, neg = 0 0392: dt=7.600000, rms=0.513 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 184 after 23 iterations, nbhd size=1, neg = 0 0393: dt=7.600000, rms=0.513 (0.051%), neg=0, invalid=762 iter 0, gcam->neg = 393 after 23 iterations, nbhd size=1, neg = 0 0394: dt=15.244635, rms=0.510 (0.556%), neg=0, invalid=762 iter 0, gcam->neg = 107 after 18 iterations, nbhd size=1, neg = 0 0395: dt=9.464789, rms=0.509 (0.212%), neg=0, invalid=762 iter 0, gcam->neg = 43 after 19 iterations, nbhd size=1, neg = 0 0396: dt=9.464789, rms=0.508 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 109 after 17 iterations, nbhd size=1, neg = 0 0397: dt=9.464789, rms=0.507 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 230 after 27 iterations, nbhd size=1, neg = 0 0398: dt=9.464789, rms=0.507 (0.081%), neg=0, invalid=762 iter 0, gcam->neg = 230 after 21 iterations, nbhd size=1, neg = 0 0399: dt=9.464789, rms=0.507 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 19 iterations, nbhd size=1, neg = 0 0400: dt=8.413793, rms=0.506 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 37 after 15 iterations, nbhd size=1, neg = 0 0401: dt=8.834356, rms=0.506 (0.070%), neg=0, invalid=762 iter 0, gcam->neg = 44 after 18 iterations, nbhd size=1, neg = 0 0402: dt=8.834356, rms=0.506 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 64 after 20 iterations, nbhd size=1, neg = 0 0403: dt=8.834356, rms=0.505 (0.043%), neg=0, invalid=762 iter 0, gcam->neg = 169 after 21 iterations, nbhd size=1, neg = 0 0404: dt=8.834356, rms=0.505 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 259 after 17 iterations, nbhd size=1, neg = 0 0405: dt=8.834356, rms=0.505 (0.070%), neg=0, invalid=762 iter 0, gcam->neg = 335 after 21 iterations, nbhd size=1, neg = 0 0406: dt=8.834356, rms=0.504 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 386 after 23 iterations, nbhd size=1, neg = 0 0407: dt=8.834356, rms=0.503 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 524 after 23 iterations, nbhd size=1, neg = 0 0408: dt=8.834356, rms=0.503 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 591 after 22 iterations, nbhd size=1, neg = 0 0409: dt=8.834356, rms=0.503 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 665 after 23 iterations, nbhd size=1, neg = 0 0410: dt=8.834356, rms=0.502 (0.072%), neg=0, invalid=762 iter 0, gcam->neg = 68 after 20 iterations, nbhd size=1, neg = 0 0411: dt=8.539326, rms=0.502 (0.071%), neg=0, invalid=762 iter 0, gcam->neg = 39 after 19 iterations, nbhd size=1, neg = 0 0412: dt=8.539326, rms=0.502 (0.097%), neg=0, invalid=762 iter 0, gcam->neg = 90 after 26 iterations, nbhd size=1, neg = 0 0413: dt=8.539326, rms=0.501 (0.044%), neg=0, invalid=762 iter 0, gcam->neg = 209 after 18 iterations, nbhd size=1, neg = 0 0414: dt=8.539326, rms=0.501 (0.012%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0415: dt=0.000000, rms=0.510 (0.231%), neg=0, invalid=762 0416: dt=0.000000, rms=0.510 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0417: dt=0.000000, rms=0.510 (0.231%), neg=0, invalid=762 0418: dt=0.000000, rms=0.510 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 iter 0, gcam->neg = 2879 after 21 iterations, nbhd size=1, neg = 0 0419: dt=1.536000, rms=0.466 (6.250%), neg=0, invalid=762 0420: dt=0.000013, rms=0.466 (0.007%), neg=0, invalid=762 0421: dt=0.000013, rms=0.466 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0422: dt=0.000000, rms=0.466 (0.267%), neg=0, invalid=762 0423: dt=0.000000, rms=0.466 (0.000%), neg=0, invalid=762 0424: dt=0.050000, rms=0.466 (-0.042%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0425: dt=32.368000, rms=0.455 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0426: dt=18.496000, rms=0.455 (0.001%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0427: dt=18.496000, rms=0.455 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0428: dt=18.496000, rms=0.455 (0.001%), neg=0, invalid=762 0429: dt=0.005645, rms=0.455 (0.000%), neg=0, invalid=762 0430: dt=0.005645, rms=0.455 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 iter 0, gcam->neg = 44 after 12 iterations, nbhd size=1, neg = 0 0431: dt=31.104000, rms=0.455 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0432: dt=36.288000, rms=0.455 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 9 iterations, nbhd size=1, neg = 0 0433: dt=103.680000, rms=0.455 (0.027%), neg=0, invalid=762 iter 0, gcam->neg = 53 after 15 iterations, nbhd size=1, neg = 0 0434: dt=331.776000, rms=0.454 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0435: dt=25.920000, rms=0.454 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0436: dt=25.920000, rms=0.454 (0.000%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0437: dt=25.920000, rms=0.454 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 iter 0, gcam->neg = 358 after 23 iterations, nbhd size=1, neg = 0 0438: dt=38.400000, rms=0.452 (0.510%), neg=0, invalid=762 iter 0, gcam->neg = 204 after 28 iterations, nbhd size=1, neg = 0 0439: dt=44.800000, rms=0.451 (0.263%), neg=0, invalid=762 iter 0, gcam->neg = 121 after 20 iterations, nbhd size=1, neg = 0 0440: dt=25.600000, rms=0.451 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 95 after 16 iterations, nbhd size=1, neg = 0 0441: dt=25.600000, rms=0.451 (-0.051%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 iter 0, gcam->neg = 39 after 16 iterations, nbhd size=1, neg = 0 0442: dt=29.886792, rms=0.450 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 76 after 32 iterations, nbhd size=2, neg = 0 0443: dt=44.800000, rms=0.450 (-0.237%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 iter 0, gcam->neg = 658 after 28 iterations, nbhd size=1, neg = 0 0444: dt=20.302521, rms=0.449 (0.869%), neg=0, invalid=762 iter 0, gcam->neg = 269 after 21 iterations, nbhd size=1, neg = 0 0445: dt=11.380952, rms=0.447 (0.285%), neg=0, invalid=762 iter 0, gcam->neg = 188 after 26 iterations, nbhd size=1, neg = 0 0446: dt=9.948718, rms=0.447 (0.113%), neg=0, invalid=762 iter 0, gcam->neg = 214 after 21 iterations, nbhd size=1, neg = 0 0447: dt=9.948718, rms=0.446 (0.135%), neg=0, invalid=762 iter 0, gcam->neg = 370 after 28 iterations, nbhd size=1, neg = 0 0448: dt=9.948718, rms=0.446 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 572 after 30 iterations, nbhd size=1, neg = 0 0449: dt=9.948718, rms=0.446 (-0.070%), neg=0, invalid=762 iter 0, gcam->neg = 126 after 39 iterations, nbhd size=2, neg = 0 0450: dt=8.769874, rms=0.446 (-0.684%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.446, neg=0, invalid=762 iter 0, gcam->neg = 132 after 21 iterations, nbhd size=1, neg = 0 0451: dt=10.029851, rms=0.445 (0.281%), neg=0, invalid=762 iter 0, gcam->neg = 82 after 30 iterations, nbhd size=1, neg = 0 0452: dt=8.689655, rms=0.445 (0.064%), neg=0, invalid=762 iter 0, gcam->neg = 72 after 23 iterations, nbhd size=1, neg = 0 0453: dt=8.689655, rms=0.444 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 154 after 27 iterations, nbhd size=1, neg = 0 0454: dt=8.689655, rms=0.444 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 270 after 40 iterations, nbhd size=1, neg = 0 0455: dt=8.689655, rms=0.444 (-0.251%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0456: dt=0.000050, rms=0.451 (0.000%), neg=0, invalid=762 0457: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762 0458: dt=0.100000, rms=0.451 (-0.048%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0459: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=762 iter 0, gcam->neg = 1646 after 21 iterations, nbhd size=1, neg = 0 0460: dt=0.819635, rms=0.430 (2.149%), neg=0, invalid=762 0461: dt=0.048000, rms=0.430 (0.015%), neg=0, invalid=762 0462: dt=0.048000, rms=0.430 (0.004%), neg=0, invalid=762 0463: dt=0.048000, rms=0.430 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0464: dt=0.320000, rms=0.429 (0.296%), neg=0, invalid=762 iter 0, gcam->neg = 99 after 12 iterations, nbhd size=1, neg = 0 0465: dt=0.448000, rms=0.427 (0.267%), neg=0, invalid=762 0466: dt=0.256000, rms=0.427 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0467: dt=0.256000, rms=0.426 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0468: dt=0.256000, rms=0.426 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 4 iterations, nbhd size=0, neg = 0 0469: dt=0.256000, rms=0.425 (0.105%), neg=0, invalid=762 iter 0, gcam->neg = 32 after 11 iterations, nbhd size=1, neg = 0 0470: dt=0.256000, rms=0.425 (0.090%), neg=0, invalid=762 0471: dt=0.112000, rms=0.425 (0.030%), neg=0, invalid=762 0472: dt=0.112000, rms=0.425 (0.017%), neg=0, invalid=762 0473: dt=0.112000, rms=0.425 (0.018%), neg=0, invalid=762 0474: dt=0.112000, rms=0.425 (0.012%), neg=0, invalid=762 0475: dt=0.112000, rms=0.425 (0.007%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 16 minutes and 6 seconds. mri_ca_register utimesec 10042.776858 mri_ca_register stimesec 11.337995 mri_ca_register ru_maxrss 1332368 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 6341181 mri_ca_register ru_majflt 8 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1696 mri_ca_register ru_oublock 65112 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 11154 mri_ca_register ru_nivcsw 37966 FSRUNTIME@ mri_ca_register 2.2684 hours 4 threads #-------------------------------------- #@# SubCort Seg Thu Feb 27 18:04:39 UTC 2020 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname beec64fd34b7 machine x86_64 setenv SUBJECTS_DIR /execute cd /execute/freesurfer/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 4 == 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 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 8.10 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.11809 (24) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (21495 voxels, overlap=0.601) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (21495 voxels, peak = 26), gca=26.1 gca peak = 0.17677 (13) mri peak = 0.11360 (24) Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (18984 voxels, overlap=0.362) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (18984 voxels, peak = 23), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.08679 (103) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (527 voxels, overlap=0.285) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (527 voxels, peak = 104), gca=104.0 gca peak = 0.16930 (96) mri peak = 0.10513 (109) Left_Pallidum (13): linear fit = 1.15 x + 0.0 (741 voxels, overlap=0.029) Left_Pallidum (13): linear fit = 1.15 x + 0.0 (741 voxels, peak = 111), gca=110.9 gca peak = 0.24553 (55) mri peak = 0.08696 (73) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (933 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (933 voxels, peak = 70), gca=69.6 gca peak = 0.30264 (59) mri peak = 0.10100 (70) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1541 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1541 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.04885 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (34728 voxels, overlap=0.892) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (34728 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.05726 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (34217 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (34217 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04216 (75) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (23698 voxels, overlap=0.119) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (23698 voxels, peak = 73), gca=73.4 gca peak = 0.11620 (58) mri peak = 0.04536 (72) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (26200 voxels, overlap=0.082) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (26200 voxels, peak = 72), gca=72.2 gca peak = 0.30970 (66) mri peak = 0.06883 (86) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1870 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1870 voxels, peak = 85), gca=85.5 gca peak = 0.15280 (69) mri peak = 0.06642 (92) Left_Caudate (11): linear fit = 1.20 x + 0.0 (1508 voxels, overlap=0.022) Left_Caudate (11): linear fit = 1.20 x + 0.0 (1508 voxels, peak = 82), gca=82.5 gca peak = 0.13902 (56) mri peak = 0.05443 (61) Left_Cerebellum_Cortex (8): linear fit = 1.10 x + 0.0 (17637 voxels, overlap=0.797) Left_Cerebellum_Cortex (8): linear fit = 1.10 x + 0.0 (17637 voxels, peak = 61), gca=61.3 gca peak = 0.14777 (55) mri peak = 0.05061 (58) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (19321 voxels, overlap=0.940) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (19321 voxels, peak = 59), gca=58.6 gca peak = 0.16765 (84) mri peak = 0.09183 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7017 voxels, overlap=0.531) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7017 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.09469 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5917 voxels, overlap=0.743) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5917 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.08060 (74) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (478 voxels, overlap=0.065) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (478 voxels, peak = 72), gca=71.5 gca peak = 0.33601 (57) mri peak = 0.10708 (73) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (404 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (404 voxels, peak = 72), gca=72.1 gca peak = 0.11131 (90) mri peak = 0.06125 (100) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (3612 voxels, overlap=0.285) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (3612 voxels, peak = 102), gca=102.2 gca peak = 0.11793 (83) mri peak = 0.08094 (102) Right_Thalamus_Proper (49): linear fit = 1.22 x + 0.0 (3632 voxels, overlap=0.013) Right_Thalamus_Proper (49): linear fit = 1.22 x + 0.0 (3632 voxels, peak = 101), gca=100.8 gca peak = 0.08324 (81) mri peak = 0.09304 (88) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1367 voxels, overlap=0.292) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1367 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.10542 (85) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1678 voxels, overlap=0.443) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1678 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.06504 (87) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12148 voxels, overlap=0.477) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12148 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.11656 (104) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (1184 voxels, overlap=0.015) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (1184 voxels, peak = 105), gca=104.6 gca peak = 0.14500 (87) mri peak = 0.10360 (108) Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1385 voxels, overlap=0.011) Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1385 voxels, peak = 104), gca=104.0 gca peak = 0.14975 (24) mri peak = 0.12451 (32) Third_Ventricle (14): linear fit = 1.23 x + 0.0 (383 voxels, overlap=0.443) Third_Ventricle (14): linear fit = 1.23 x + 0.0 (383 voxels, peak = 29), gca=29.4 gca peak = 0.19357 (14) mri peak = 0.11563 (23) Fourth_Ventricle (15): linear fit = 1.39 x + 0.0 (1081 voxels, overlap=0.585) Fourth_Ventricle (15): linear fit = 1.39 x + 0.0 (1081 voxels, peak = 20), gca=19.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.25 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 Left_Pallidum too bright - rescaling by 0.928 (from 1.155) to 102.9 (was 110.9) Right_Pallidum too bright - rescaling by 0.989 (from 1.095) to 102.9 (was 104.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15813 (24) mri peak = 0.11809 (24) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (21495 voxels, overlap=0.849) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (21495 voxels, peak = 23), gca=23.4 gca peak = 0.14041 (19) mri peak = 0.11360 (24) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (18984 voxels, overlap=0.710) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (18984 voxels, peak = 22), gca=21.6 gca peak = 0.21828 (101) mri peak = 0.08679 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (527 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (527 voxels, peak = 102), gca=101.5 gca peak = 0.16291 (101) mri peak = 0.10513 (109) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (741 voxels, overlap=0.419) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (741 voxels, peak = 108), gca=107.6 gca peak = 0.21457 (70) mri peak = 0.08696 (73) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (933 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (933 voxels, peak = 70), gca=70.0 gca peak = 0.30019 (69) mri peak = 0.10100 (70) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1541 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1541 voxels, peak = 67), gca=67.3 gca peak = 0.07517 (106) mri peak = 0.04885 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34728 voxels, overlap=0.957) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34728 voxels, peak = 107), gca=106.5 gca peak = 0.07840 (106) mri peak = 0.05726 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34217 voxels, overlap=0.811) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34217 voxels, peak = 106), gca=106.0 gca peak = 0.07793 (73) mri peak = 0.04216 (75) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (23698 voxels, overlap=0.959) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (23698 voxels, peak = 72), gca=71.9 gca peak = 0.09556 (72) mri peak = 0.04536 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (26200 voxels, overlap=0.958) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (26200 voxels, peak = 71), gca=70.9 gca peak = 0.21562 (85) mri peak = 0.06883 (86) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1870 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1870 voxels, peak = 85), gca=85.0 gca peak = 0.12897 (82) mri peak = 0.06642 (92) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1508 voxels, overlap=0.997) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1508 voxels, peak = 83), gca=83.2 gca peak = 0.12615 (61) mri peak = 0.05443 (61) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (17637 voxels, overlap=0.987) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (17637 voxels, peak = 63), gca=62.5 gca peak = 0.13882 (58) mri peak = 0.05061 (58) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (19321 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (19321 voxels, peak = 57), gca=57.1 gca peak = 0.15948 (90) mri peak = 0.09183 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7017 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7017 voxels, peak = 92), gca=92.2 gca peak = 0.15241 (90) mri peak = 0.09469 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5917 voxels, overlap=0.966) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5917 voxels, peak = 91), gca=91.3 gca peak = 0.28676 (73) mri peak = 0.08060 (74) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (478 voxels, overlap=1.024) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (478 voxels, peak = 76), gca=75.6 gca peak = 0.31977 (72) mri peak = 0.10708 (73) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (404 voxels, overlap=0.994) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (404 voxels, peak = 74), gca=73.8 gca peak = 0.10515 (102) mri peak = 0.06125 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3612 voxels, overlap=0.927) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3612 voxels, peak = 103), gca=102.5 gca peak = 0.10133 (98) mri peak = 0.08094 (102) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3632 voxels, overlap=0.943) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3632 voxels, peak = 98), gca=98.0 gca peak = 0.07912 (84) mri peak = 0.09304 (88) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1367 voxels, overlap=0.756) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1367 voxels, peak = 83), gca=82.7 gca peak = 0.08499 (85) mri peak = 0.10542 (85) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1678 voxels, overlap=0.804) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1678 voxels, peak = 86), gca=86.3 gca peak = 0.07936 (88) mri peak = 0.06504 (87) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12148 voxels, overlap=0.892) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12148 voxels, peak = 89), gca=89.3 gca peak = 0.11554 (103) mri peak = 0.11656 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1184 voxels, overlap=0.734) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1184 voxels, peak = 103), gca=103.0 gca peak = 0.15010 (102) mri peak = 0.10360 (108) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1385 voxels, overlap=0.865) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1385 voxels, peak = 104), gca=103.5 gca peak = 0.12950 (31) mri peak = 0.12451 (32) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (383 voxels, overlap=0.855) Third_Ventricle (14): linear fit = 1.01 x + 0.0 (383 voxels, peak = 31), gca=31.5 gca peak = 0.14735 (21) mri peak = 0.11563 (23) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (1081 voxels, overlap=0.799) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (1081 voxels, peak = 22), gca=21.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16283 (33) gca peak Left_Thalamus = 0.36646 (104) gca peak CSF = 0.21405 (49) gca peak Left_Accumbens_area = 0.63807 (74) gca peak Left_undetermined = 0.96707 (30) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12577 (35) gca peak Right_Inf_Lat_Vent = 0.19572 (29) gca peak Right_Accumbens_area = 0.29821 (84) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14507 (37) gca peak Fifth_Ventricle = 0.75707 (42) gca peak WM_hypointensities = 0.08421 (78) gca peak non_WM_hypointensities = 0.07502 (56) gca peak Optic_Chiasm = 0.49859 (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 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.958 (from 1.065) to 103.1 (was 107.6) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 65464 voxels changed in iteration 0 of unlikely voxel relabeling 138 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 51124 gm and wm labels changed (%36 to gray, %64 to white out of all changed labels) 407 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 78816 changed. image ll: -2.177, PF=0.500 pass 2: 19891 changed. image ll: -2.176, PF=0.500 pass 3: 6866 changed. pass 4: 2850 changed. 47497 voxels changed in iteration 0 of unlikely voxel relabeling 210 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7078 voxels changed in iteration 0 of unlikely voxel relabeling 119 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6799 voxels changed in iteration 0 of unlikely voxel relabeling 114 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5998 voxels changed in iteration 0 of unlikely voxel relabeling 51 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3055.521720 mri_ca_label stimesec 1.382742 mri_ca_label ru_maxrss 2102880 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 715683 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 528 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 691 mri_ca_label ru_nivcsw 2702 auto-labeling took 49 minutes and 51 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /execute/freesurfer/mri/transforms/cc_up.lta freesurfer will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /execute/freesurfer/mri/transforms/cc_up.lta reading aseg from /execute/freesurfer/mri/aseg.auto_noCCseg.mgz reading norm from /execute/freesurfer/mri/norm.mgz 25705 voxels in left wm, 26236 in right wm, xrange [125, 133] searching rotation angles z=[-7 7], y=[-8 6] searching scale 1 Z rot 6.9 global minimum found at slice 128.3, rotations (-0.78, 0.11) final transformation (x=128.3, yr=-0.777, zr=0.106): 0.99991 -0.00185 -0.01357 1.19064; 0.00185 1.00000 -0.00003 38.76572; 0.01357 -0.00000 0.99991 30.26808; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 89 96 eigenvectors: 0.01531 0.00916 0.99984; -0.10544 -0.99437 0.01073; 0.99431 -0.10559 -0.01426; error in mid anterior detected - correcting... writing aseg with callosum to /execute/freesurfer/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Thu Feb 27 18:55:00 UTC 2020 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Feb 27 18:55:00 UTC 2020 /execute/freesurfer/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 795 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 107 gm peak at 77 (77), valley at 57 (57) csf peak at 23, 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 109 gm peak at 77 (77), valley at 44 (44) csf peak at 22, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 40 seconds. #-------------------------------------------- #@# Mask BFS Thu Feb 27 18:57:41 UTC 2020 /execute/freesurfer/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1718077 voxels in mask (pct= 10.24) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Feb 27 18:57:44 UTC 2020 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.8 +- 5.9 [79.0 --> 125.0] GM (72.0) : 69.6 +- 12.3 [30.0 --> 95.0] setting bottom of white matter range to 81.8 setting top of gray matter range to 94.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4206 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5474 filled 1896 bright non-wm voxels segmented. 2827 diagonally connected voxels added... white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.42 minutes reading wm segmentation from wm.seg.mgz... 573 voxels added to wm to prevent paths from MTL structures to cortex 11638 additional wm voxels added 0 additional wm voxels added SEG EDIT: 180788 voxels turned on, 41893 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 44 found - 44 modified | TOTAL: 44 pass 2 (xy+): 0 found - 44 modified | TOTAL: 44 pass 1 (xy-): 31 found - 31 modified | TOTAL: 75 pass 2 (xy-): 0 found - 31 modified | TOTAL: 75 pass 1 (yz+): 53 found - 53 modified | TOTAL: 128 pass 2 (yz+): 0 found - 53 modified | TOTAL: 128 pass 1 (yz-): 49 found - 49 modified | TOTAL: 177 pass 2 (yz-): 0 found - 49 modified | TOTAL: 177 pass 1 (xz+): 41 found - 41 modified | TOTAL: 218 pass 2 (xz+): 0 found - 41 modified | TOTAL: 218 pass 1 (xz-): 39 found - 39 modified | TOTAL: 257 pass 2 (xz-): 0 found - 39 modified | TOTAL: 257 Iteration Number : 1 pass 1 (+++): 17 found - 17 modified | TOTAL: 17 pass 2 (+++): 0 found - 17 modified | TOTAL: 17 pass 1 (+++): 22 found - 22 modified | TOTAL: 39 pass 2 (+++): 0 found - 22 modified | TOTAL: 39 pass 1 (+++): 13 found - 13 modified | TOTAL: 52 pass 2 (+++): 0 found - 13 modified | TOTAL: 52 pass 1 (+++): 17 found - 17 modified | TOTAL: 69 pass 2 (+++): 0 found - 17 modified | TOTAL: 69 Iteration Number : 1 pass 1 (++): 83 found - 83 modified | TOTAL: 83 pass 2 (++): 0 found - 83 modified | TOTAL: 83 pass 1 (+-): 102 found - 102 modified | TOTAL: 185 pass 2 (+-): 0 found - 102 modified | TOTAL: 185 pass 1 (--): 92 found - 92 modified | TOTAL: 277 pass 2 (--): 0 found - 92 modified | TOTAL: 277 pass 1 (-+): 97 found - 97 modified | TOTAL: 374 pass 2 (-+): 0 found - 97 modified | TOTAL: 374 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 9 found - 9 modified | TOTAL: 16 pass 2 (xy-): 0 found - 9 modified | TOTAL: 16 pass 1 (yz+): 10 found - 10 modified | TOTAL: 26 pass 2 (yz+): 0 found - 10 modified | TOTAL: 26 pass 1 (yz-): 2 found - 2 modified | TOTAL: 28 pass 2 (yz-): 0 found - 2 modified | TOTAL: 28 pass 1 (xz+): 11 found - 11 modified | TOTAL: 39 pass 2 (xz+): 0 found - 11 modified | TOTAL: 39 pass 1 (xz-): 1 found - 1 modified | TOTAL: 40 pass 2 (xz-): 0 found - 1 modified | TOTAL: 40 Iteration Number : 2 pass 1 (+++): 3 found - 3 modified | TOTAL: 3 pass 2 (+++): 0 found - 3 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 4 found - 4 modified | TOTAL: 7 pass 2 (+-): 1 found - 5 modified | TOTAL: 8 pass 3 (+-): 0 found - 5 modified | TOTAL: 8 pass 1 (--): 5 found - 5 modified | TOTAL: 13 pass 2 (--): 0 found - 5 modified | TOTAL: 13 pass 1 (-+): 5 found - 5 modified | TOTAL: 18 pass 2 (-+): 0 found - 5 modified | TOTAL: 18 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 765 (out of 629417: 0.121541) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Feb 27 18:59:38 UTC 2020 /execute/freesurfer/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01470 0.04471 0.00686 -10.44992; -0.03703 1.00802 0.22818 -1.37637; 0.00377 -0.20013 0.91919 25.75654; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1749 (min = 350, max = 1400), aspect = 0.56 (min = 0.10, max = 0.75) need search nearby using seed (124, 110, 98), TAL = (4.0, -30.0, 18.0) talairach voxel to voxel transform 0.98393 -0.04298 0.00333 10.13704; 0.03532 0.94391 -0.23458 7.71031; 0.00365 0.20569 1.03683 -26.38383; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 110, 98) --> (4.0, -30.0, 18.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (4.00, -30.00, 18.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -30.00, 18.00) SRC: (110.03, 92.29, 98.24) search lh wm seed point around talairach space (-14.00, -30.00, 18.00), SRC: (145.45, 93.57, 98.37) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Feb 27 19:00:10 UTC 2020 /execute/freesurfer/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 0 found - 0 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 0 found - 0 modified | TOTAL: 7 pass 1 (xz+): 3 found - 3 modified | TOTAL: 10 pass 2 (xz+): 0 found - 3 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 307735: 0.004549) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 801 vertices, 878 faces slice 50: 5799 vertices, 6008 faces slice 60: 13997 vertices, 14352 faces slice 70: 25341 vertices, 25740 faces slice 80: 35675 vertices, 36021 faces slice 90: 45750 vertices, 46110 faces slice 100: 56111 vertices, 56546 faces slice 110: 67117 vertices, 67510 faces slice 120: 77892 vertices, 78295 faces slice 130: 88722 vertices, 89125 faces slice 140: 99265 vertices, 99679 faces slice 150: 107949 vertices, 108253 faces slice 160: 114802 vertices, 115092 faces slice 170: 122200 vertices, 122497 faces slice 180: 128508 vertices, 128784 faces slice 190: 133671 vertices, 133885 faces slice 200: 136453 vertices, 136550 faces slice 210: 136528 vertices, 136592 faces slice 220: 136528 vertices, 136592 faces slice 230: 136528 vertices, 136592 faces slice 240: 136528 vertices, 136592 faces slice 250: 136528 vertices, 136592 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 136528 voxel in cpt #1: X=-64 [v=136528,e=409776,f=273184] located at (-27.888836, -16.307350, 33.624149) For the whole surface: X=-64 [v=136528,e=409776,f=273184] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu Feb 27 19:00:16 UTC 2020 /execute/freesurfer/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 4 found - 4 modified | TOTAL: 5 pass 2 (yz+): 0 found - 4 modified | TOTAL: 5 pass 1 (yz-): 2 found - 2 modified | TOTAL: 7 pass 2 (yz-): 0 found - 2 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 0 found - 0 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 307199: 0.004232) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 1782 vertices, 1930 faces slice 50: 8363 vertices, 8642 faces slice 60: 17437 vertices, 17797 faces slice 70: 29229 vertices, 29621 faces slice 80: 39776 vertices, 40162 faces slice 90: 50231 vertices, 50600 faces slice 100: 61330 vertices, 61752 faces slice 110: 72824 vertices, 73243 faces slice 120: 83762 vertices, 84150 faces slice 130: 94604 vertices, 95001 faces slice 140: 105525 vertices, 105898 faces slice 150: 113891 vertices, 114166 faces slice 160: 120191 vertices, 120488 faces slice 170: 127583 vertices, 127863 faces slice 180: 133903 vertices, 134161 faces slice 190: 138547 vertices, 138764 faces slice 200: 140630 vertices, 140710 faces slice 210: 140630 vertices, 140710 faces slice 220: 140630 vertices, 140710 faces slice 230: 140630 vertices, 140710 faces slice 240: 140630 vertices, 140710 faces slice 250: 140630 vertices, 140710 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 140630 voxel in cpt #1: X=-80 [v=140630,e=422130,f=281420] located at (27.227283, -19.248865, 32.097839) For the whole surface: X=-80 [v=140630,e=422130,f=281420] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Feb 27 19:00:21 UTC 2020 /execute/freesurfer/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Thu Feb 27 19:00:21 UTC 2020 /execute/freesurfer/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 3320 of (3320 3323) to complete... Waiting for PID 3323 of (3320 3323) to complete... PIDs (3320 3323) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Thu Feb 27 19:00:26 UTC 2020 /execute/freesurfer/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Thu Feb 27 19:00:26 UTC 2020 /execute/freesurfer/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 3368 of (3368 3371) to complete... Waiting for PID 3371 of (3368 3371) to complete... PIDs (3368 3371) completed and logs appended. #-------------------------------------------- #@# QSphere lh Thu Feb 27 19:01:06 UTC 2020 /execute/freesurfer/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Thu Feb 27 19:01:06 UTC 2020 /execute/freesurfer/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 3416 of (3416 3419) to complete... Waiting for PID 3419 of (3416 3419) to complete... PIDs (3416 3419) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Thu Feb 27 19:04:43 UTC 2020 /execute/freesurfer/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Thu Feb 27 19:04:43 UTC 2020 /execute/freesurfer/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Thu Feb 27 19:04:43 UTC 2020 mris_fix_topology -rusage /execute/freesurfer/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 freesurfer lh #@# Fix Topology rh Thu Feb 27 19:04:43 UTC 2020 mris_fix_topology -rusage /execute/freesurfer/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 freesurfer rh Waiting for PID 3500 of (3500 3503) to complete... Waiting for PID 3503 of (3500 3503) to complete... PIDs (3500 3503) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 134155 - 402459 + 268306 = 2 --> 0 holes F =2V-4: 268306 = 268310-4 (0) 2E=3F: 804918 = 804918 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 136396 - 409182 + 272788 = 2 --> 0 holes F =2V-4: 272788 = 272792-4 (0) 2E=3F: 818364 = 818364 (0) total defect index = 0 /execute/freesurfer/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 23 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /execute/freesurfer/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 84 intersecting 001: 27 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Feb 27 19:38:00 UTC 2020 /execute/freesurfer/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs freesurfer lh #-------------------------------------------- #@# Make White Surf rh Thu Feb 27 19:38:00 UTC 2020 /execute/freesurfer/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs freesurfer rh Waiting for PID 3607 of (3607 3610) to complete... Waiting for PID 3610 of (3607 3610) to complete... PIDs (3607 3610) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Thu Feb 27 19:41:44 UTC 2020 /execute/freesurfer/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Thu Feb 27 19:41:44 UTC 2020 /execute/freesurfer/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 3656 of (3656 3659) to complete... Waiting for PID 3659 of (3656 3659) to complete... PIDs (3656 3659) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Thu Feb 27 19:41:49 UTC 2020 /execute/freesurfer/scripts mris_inflate -rusage /execute/freesurfer/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Thu Feb 27 19:41:49 UTC 2020 /execute/freesurfer/scripts mris_inflate -rusage /execute/freesurfer/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 3705 of (3705 3708) to complete... Waiting for PID 3708 of (3705 3708) to complete... PIDs (3705 3708) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Thu Feb 27 19:42:27 UTC 2020 /execute/freesurfer/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Thu Feb 27 19:42:27 UTC 2020 /execute/freesurfer/surf mris_curvature -w rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /execute/freesurfer/surf reconbatchjobs /execute/freesurfer/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 3786 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3789 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3792 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3795 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3798 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3801 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3804 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3807 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3810 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3813 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3816 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... Waiting for PID 3819 of (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) to complete... PIDs (3786 3789 3792 3795 3798 3801 3804 3807 3810 3813 3816 3819) completed and logs appended. /execute/freesurfer/surf Cannot find rh.white.H Linux beec64fd34b7 4.15.0-1054-aws #56-Ubuntu SMP Thu Nov 7 16:15:59 UTC 2019 x86_64 GNU/Linux recon-all -s freesurfer exited with ERRORS at Thu Feb 27 19:43:25 UTC 2020 For more details, see the log file /execute/freesurfer/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting