returncodereturncode0prevcwd/home/pkashyap/PK/PK3stderrstdoutSubject 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 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 Actual FREESURFER_HOME /opt/freesurfer Linux roxy 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts/recon-all.local-copy' /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg mri_convert /home/pkashyap/data/subj01/anat/t11_sanlm.nii.gz /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig/001.mgz mri_convert.bin /home/pkashyap/data/subj01/anat/t11_sanlm.nii.gz /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/pkashyap/data/subj01/anat/t11_sanlm.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Jul 22 11:54:33 EDT 2019 Found 1 runs /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/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 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig/001.mgz /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg mri_convert /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz --conform mri_convert.bin /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz... mri_add_xform_to_header -c /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/transforms/talairach.xfm /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jul 22 11:54:44 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri /opt/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 roxy 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Mon Jul 22 11:54:44 EDT 2019 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.23813 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23813/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.23813/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.23813/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jul 22 11:54:47 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.23813/nu0.mnc ./tmp.mri_nu_correct.mni.23813/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23813/0/ -iterations 1000 -distance 50 [pkashyap@roxy:/tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/] [2019-07-22 11:54:47] running: /opt/freesurfer/6.0/mni/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.23813/0/ ./tmp.mri_nu_correct.mni.23813/nu0.mnc ./tmp.mri_nu_correct.mni.23813/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 Number of iterations: 35 CV of field change: 0.000999342 mri_convert ./tmp.mri_nu_correct.mni.23813/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.23813/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.23813/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... Mon Jul 22 11:56:22 EDT 2019 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 Mon Jul 22 11:56:22 EDT 2019 Ended at Mon Jul 22 11:57:22 EDT 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jul 22 11:57:24 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7244, pval=0.4932 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/transforms/talairach_avi.log tal_QC_AZS /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/transforms/talairach_avi.log TalAviQA: 0.97025 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Mon Jul 22 11:57:24 EDT 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri /opt/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 roxy 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Mon Jul 22 11:57:24 EDT 2019 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.29116 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29116/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29116/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.29116/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jul 22 11:57:27 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.29116/nu0.mnc ./tmp.mri_nu_correct.mni.29116/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29116/0/ [pkashyap@roxy:/tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/] [2019-07-22 11:57:28] running: /opt/freesurfer/6.0/mni/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.29116/0/ ./tmp.mri_nu_correct.mni.29116/nu0.mnc ./tmp.mri_nu_correct.mni.29116/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 Number of iterations: 21 CV of field change: 0.000979497 -------------------------------------------------------- Iteration 2 Mon Jul 22 11:58:30 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.29116/nu1.mnc ./tmp.mri_nu_correct.mni.29116/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.29116/1/ [pkashyap@roxy:/tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/] [2019-07-22 11:58:30] running: /opt/freesurfer/6.0/mni/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.29116/1/ ./tmp.mri_nu_correct.mni.29116/nu1.mnc ./tmp.mri_nu_correct.mni.29116/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 Number of iterations: 17 CV of field change: 0.000955938 mri_binarize --i ./tmp.mri_nu_correct.mni.29116/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29116/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.29116/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29116/ones.mgz sysname Linux hostname roxy machine x86_64 user pkashyap input ./tmp.mri_nu_correct.mni.29116/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.29116/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.29116/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29116/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29116/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.29116/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29116/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29116/input.mean.dat sysname Linux hostname roxy machine x86_64 user pkashyap UseRobust 0 Loading ./tmp.mri_nu_correct.mni.29116/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.29116/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.29116/ones.mgz --i ./tmp.mri_nu_correct.mni.29116/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29116/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29116/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.29116/ones.mgz --i ./tmp.mri_nu_correct.mni.29116/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29116/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29116/output.mean.dat sysname Linux hostname roxy machine x86_64 user pkashyap UseRobust 0 Loading ./tmp.mri_nu_correct.mni.29116/ones.mgz Loading ./tmp.mri_nu_correct.mni.29116/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.29116/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.29116/nu2.mnc ./tmp.mri_nu_correct.mni.29116/nu2.mnc mul 1.07901292646265421384 Saving result to './tmp.mri_nu_correct.mni.29116/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.29116/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.29116/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.29116/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 13 seconds. mapping ( 2, 96) to ( 3, 110) Mon Jul 22 12:00:23 EDT 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Jul 22 12:00:23 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/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 1.02368 -0.04382 -0.07692 3.66923; 0.07255 1.03925 0.13526 -40.90398; 0.05008 -0.04174 1.09100 -11.82822; 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 = 16 Starting OpenSpline(): npoints = 16 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 51 (51), valley at 34 (34) 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 50 (50), valley at 33 (33) csf peak at 25, setting threshold to 41 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 19 seconds. #-------------------------------------------- #@# Skull Stripping Mon Jul 22 12:03:43 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_em_register -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /opt/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 = 64 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/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=11.0 skull bounding box = (41, 30, 25) --> (213, 223, 225) using (98, 94, 125) as brain centroid... mean wm in atlas = 108, using box (77,70,100) --> (119, 117,149) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 106 +- 6.2 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.384 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.389106 @ (0.000, 0.000, 0.000) max log p = -4.209772 @ (-4.545, 4.545, -13.636) max log p = -4.005515 @ (2.273, 2.273, -2.273) max log p = -3.988428 @ (1.136, -1.136, -1.136) max log p = -3.986584 @ (1.705, 0.568, 2.841) max log p = -3.986584 @ (0.000, 0.000, 0.000) Found translation: (0.6, 6.2, -14.2): log p = -3.987 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.867, old_max_log_p =-3.987 (thresh=-4.0) 0.99144 -0.01959 0.12941 -11.89796; 0.00000 1.22567 0.14032 -34.48190; -0.14032 -0.15998 1.05669 17.89030; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.867, old_max_log_p =-3.867 (thresh=-3.9) 0.99144 -0.01959 0.12941 -11.89796; 0.00000 1.22567 0.14032 -34.48190; -0.14032 -0.15998 1.05669 17.89030; 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=-3.741, old_max_log_p =-3.867 (thresh=-3.9) 0.99747 -0.05632 0.05827 -1.03478; 0.03656 1.18302 0.10496 -30.84233; -0.07862 -0.12151 1.08687 1.60023; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.741, old_max_log_p =-3.741 (thresh=-3.7) 0.99747 -0.05632 0.05827 -1.03478; 0.03656 1.18302 0.10496 -30.84233; -0.07862 -0.12151 1.08687 1.60023; 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=-3.732, old_max_log_p =-3.741 (thresh=-3.7) 0.99925 -0.05547 0.04945 0.19556; 0.03729 1.18674 0.09633 -29.88100; -0.06997 -0.11198 1.08558 -0.11633; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.731, old_max_log_p =-3.732 (thresh=-3.7) 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 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 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.731 (old=-4.384) transform before final EM align: 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 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 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.00042 -0.05554 0.04951 0.04946; 0.03738 1.18952 0.09656 -30.28426; -0.06997 -0.11198 1.08558 -0.11633; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 315462.468000 mri_em_register stimesec 2331.496000 mri_em_register ru_maxrss 610212 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 13158448 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 240767072 mri_em_register ru_nivcsw 45332120 registration took 327 minutes and 41 seconds. mri_watershed -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mri_watershed.dat -T1 -brain_atlas /opt/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=125 y=108 z=123 r=79 first estimation of the main basin volume: 2079954 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=108, y=90, z=85, Imax=255 CSF=21, 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=491402774 voxels, voxel volume =1.000 = 491402774 mmm3 = 491402.784 cm3 done. PostAnalyze...Basin Prior 70 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=126,y=114, z=117, r=9759 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45260 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1037473261 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1097072607 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1104201296 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1076313132 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1071832918 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 5, 24, 46 after analyzing : 4, 18, 25, 25 RIGHT_CER before analyzing : 4, 5, 24, 47 after analyzing : 4, 18, 25, 25 LEFT_CER before analyzing : 4, 5, 20, 47 after analyzing : 4, 18, 25, 25 RIGHT_BRAIN before analyzing : 5, 7, 23, 46 after analyzing : 5, 19, 25, 25 LEFT_BRAIN before analyzing : 4, 5, 24, 46 after analyzing : 4, 18, 25, 25 OTHER before analyzing : 4, 10, 72, 91 after analyzing : 4, 51, 72, 61 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...73 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.010 curvature mean = 73.711, std = 7.682 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.30, sigma = 4.85 after rotation: sse = 3.30, sigma = 4.85 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.34, its var is 3.83 before Erosion-Dilatation 0.05% 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...29 iterations mri_strip_skull: done peeling brain Brain Size = 1726483 voxels, voxel volume = 1.000 mm3 = 1726483 mmm3 = 1726.483 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 169.544000 mri_watershed stimesec 3.872000 mri_watershed ru_maxrss 833132 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 492828 mri_watershed ru_majflt 3 mri_watershed ru_nswap 0 mri_watershed ru_inblock 320 mri_watershed ru_oublock 2664 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 104187 mri_watershed ru_nivcsw 25133 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Jul 22 17:32:10 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_em_register -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/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 = 64 == reading 1 input volumes... logging results to talairach.log reading '/opt/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=20.0 skull bounding box = (54, 48, 42) --> (199, 167, 211) using (102, 88, 127) as brain centroid... mean wm in atlas = 107, using box (84,73,106) --> (119, 102,147) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 105 +- 5.5 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.134 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.949180 @ (-9.091, 9.091, -9.091) max log p = -3.697943 @ (4.545, -4.545, -4.545) max log p = -3.525069 @ (2.273, 2.273, -2.273) max log p = -3.525069 @ (0.000, 0.000, 0.000) max log p = -3.523264 @ (2.841, -1.705, -0.568) max log p = -3.512102 @ (-0.852, 1.420, 1.420) Found translation: (-0.3, 6.5, -15.1): log p = -3.512 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.403, old_max_log_p =-3.512 (thresh=-3.5) 0.99144 -0.15011 0.00000 17.72783; 0.12074 1.05465 0.00000 -14.96409; 0.00000 0.00000 1.00000 -15.05682; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.403, old_max_log_p =-3.403 (thresh=-3.4) 0.99144 -0.15011 0.00000 17.72783; 0.12074 1.05465 0.00000 -14.96409; 0.00000 0.00000 1.00000 -15.05682; 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=-3.236, old_max_log_p =-3.403 (thresh=-3.4) 0.99650 -0.08309 0.03556 5.24302; 0.05871 1.12061 0.06447 -22.29206; -0.04206 -0.06278 1.01538 -2.61306; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.231, old_max_log_p =-3.236 (thresh=-3.2) 0.99650 -0.08309 0.03556 5.24302; 0.05871 1.12061 0.06447 -22.29206; -0.04128 -0.06160 0.99634 -0.58698; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.230, old_max_log_p =-3.231 (thresh=-3.2) 0.99650 -0.08309 0.03556 5.24302; 0.05871 1.12061 0.06447 -22.29206; -0.04205 -0.06276 1.01502 -2.57506; 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=-3.190, old_max_log_p =-3.230 (thresh=-3.2) 0.99262 -0.08341 0.04374 5.29316; 0.05799 1.11813 0.08084 -23.41091; -0.05129 -0.08054 1.01708 0.82326; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.189, old_max_log_p =-3.190 (thresh=-3.2) 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 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 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.189 (old=-4.134) transform before final EM align: 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 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 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.8 tol 0.000000 final transform: 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 363176.256000 mri_em_register stimesec 2727.664000 mri_em_register ru_maxrss 599076 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 16099480 mri_em_register ru_majflt 2 mri_em_register ru_nswap 0 mri_em_register ru_inblock 272 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 273173103 mri_em_register ru_nivcsw 46635831 registration took 342 minutes and 42 seconds. #-------------------------------------- #@# CA Normalize Mon Jul 22 23:14:51 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/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 '/opt/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=20.0 skull bounding box = (54, 48, 42) --> (199, 167, 211) using (102, 88, 127) as brain centroid... mean wm in atlas = 107, using box (84,73,106) --> (119, 102,147) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 105 +- 5.5 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 246344 sample points... INFO: compute sample coordinates transform 0.99146 -0.08331 0.04369 5.43548; 0.05799 1.11813 0.08084 -23.41091; -0.05135 -0.08063 1.01827 0.70065; 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 (125, 52, 42) --> (194, 156, 206) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 4 of 7044 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (60, 54, 40) --> (127, 160, 205) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 1 of 7009 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 131, 66) --> (181, 167, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 486 of 510 (95.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 131, 62) --> (131, 169, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 137 of 303 (45.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 122, 100) --> (148, 185, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 75 of 259 (29.0%) samples deleted using 15125 total control points for intensity normalization... bias field = 0.958 +- 0.037 11 of 14422 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 52, 42) --> (194, 156, 206) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 3 of 7588 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (60, 54, 40) --> (127, 160, 205) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 7647 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 131, 66) --> (181, 167, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 568 of 570 (99.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 131, 62) --> (131, 169, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 319 of 353 (90.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 122, 100) --> (148, 185, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 315 of 417 (75.5%) samples deleted using 16575 total control points for intensity normalization... bias field = 1.024 +- 0.039 12 of 15286 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 52, 42) --> (194, 156, 206) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 4 of 7656 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (60, 54, 40) --> (127, 160, 205) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 12 of 7728 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 131, 66) --> (181, 167, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 617 of 617 (100.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 131, 62) --> (131, 169, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 374 of 385 (97.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 122, 100) --> (148, 185, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 309 of 383 (80.7%) samples deleted using 16769 total control points for intensity normalization... bias field = 1.028 +- 0.038 11 of 15285 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 37 seconds. #-------------------------------------- #@# CA Reg Mon Jul 22 23:17:29 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_ca_register -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/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 = 64 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.14 (predicted orig area = 7.0) 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=0.888, neg=0, invalid=762 0001: dt=221.952000, rms=0.840 (5.411%), neg=0, invalid=762 0002: dt=314.636872, rms=0.820 (2.337%), neg=0, invalid=762 0003: dt=152.483221, rms=0.813 (0.910%), neg=0, invalid=762 0004: dt=517.888000, rms=0.804 (1.009%), neg=0, invalid=762 0005: dt=129.472000, rms=0.801 (0.437%), neg=0, invalid=762 0006: dt=1183.744000, rms=0.794 (0.812%), neg=0, invalid=762 0007: dt=129.472000, rms=0.789 (0.619%), neg=0, invalid=762 0008: dt=517.888000, rms=0.786 (0.387%), neg=0, invalid=762 0009: dt=129.472000, rms=0.786 (0.098%), neg=0, invalid=762 0010: dt=129.472000, rms=0.785 (0.087%), neg=0, invalid=762 0011: dt=129.472000, rms=0.784 (0.154%), neg=0, invalid=762 0012: dt=129.472000, rms=0.782 (0.206%), neg=0, invalid=762 0013: dt=129.472000, rms=0.780 (0.251%), neg=0, invalid=762 0014: dt=129.472000, rms=0.778 (0.284%), neg=0, invalid=762 0015: dt=129.472000, rms=0.776 (0.294%), neg=0, invalid=762 0016: dt=129.472000, rms=0.773 (0.297%), neg=0, invalid=762 0017: dt=129.472000, rms=0.771 (0.295%), neg=0, invalid=762 0018: dt=129.472000, rms=0.769 (0.286%), neg=0, invalid=762 0019: dt=129.472000, rms=0.767 (0.269%), neg=0, invalid=762 0020: dt=129.472000, rms=0.765 (0.260%), neg=0, invalid=762 0021: dt=129.472000, rms=0.763 (0.241%), neg=0, invalid=762 0022: dt=129.472000, rms=0.761 (0.211%), neg=0, invalid=762 0023: dt=129.472000, rms=0.760 (0.203%), neg=0, invalid=762 0024: dt=129.472000, rms=0.758 (0.188%), neg=0, invalid=762 0025: dt=129.472000, rms=0.757 (0.164%), neg=0, invalid=762 0026: dt=129.472000, rms=0.756 (0.153%), neg=0, invalid=762 0027: dt=129.472000, rms=0.755 (0.150%), neg=0, invalid=762 0028: dt=129.472000, rms=0.754 (0.150%), neg=0, invalid=762 0029: dt=129.472000, rms=0.753 (0.142%), neg=0, invalid=762 0030: dt=129.472000, rms=0.752 (0.134%), neg=0, invalid=762 0031: dt=129.472000, rms=0.751 (0.118%), neg=0, invalid=762 0032: dt=129.472000, rms=0.750 (0.111%), neg=0, invalid=762 0033: dt=1183.744000, rms=0.749 (0.075%), neg=0, invalid=762 0034: dt=1183.744000, rms=0.749 (-3.415%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.750, neg=0, invalid=762 0035: dt=129.472000, rms=0.749 (0.203%), neg=0, invalid=762 0036: dt=295.936000, rms=0.748 (0.052%), neg=0, invalid=762 0037: dt=295.936000, rms=0.748 (0.094%), neg=0, invalid=762 0038: dt=295.936000, rms=0.747 (0.055%), neg=0, invalid=762 0039: dt=295.936000, rms=0.747 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.754, neg=0, invalid=762 0040: dt=251.387387, rms=0.739 (1.933%), neg=0, invalid=762 0041: dt=205.319797, rms=0.725 (1.957%), neg=0, invalid=762 0042: dt=76.469185, rms=0.718 (0.860%), neg=0, invalid=762 0043: dt=145.152000, rms=0.714 (0.538%), neg=0, invalid=762 0044: dt=124.416000, rms=0.711 (0.548%), neg=0, invalid=762 0045: dt=82.944000, rms=0.708 (0.360%), neg=0, invalid=762 0046: dt=145.152000, rms=0.705 (0.430%), neg=0, invalid=762 0047: dt=69.084932, rms=0.703 (0.315%), neg=0, invalid=762 0048: dt=145.152000, rms=0.700 (0.386%), neg=0, invalid=762 0049: dt=76.646707, rms=0.699 (0.202%), neg=0, invalid=762 0050: dt=76.646707, rms=0.697 (0.224%), neg=0, invalid=762 0051: dt=76.646707, rms=0.695 (0.312%), neg=0, invalid=762 0052: dt=76.646707, rms=0.692 (0.470%), neg=0, invalid=762 0053: dt=76.646707, rms=0.688 (0.496%), neg=0, invalid=762 0054: dt=76.646707, rms=0.684 (0.585%), neg=0, invalid=762 0055: dt=76.646707, rms=0.681 (0.511%), neg=0, invalid=762 0056: dt=76.646707, rms=0.677 (0.527%), neg=0, invalid=762 0057: dt=76.646707, rms=0.674 (0.452%), neg=0, invalid=762 0058: dt=76.646707, rms=0.671 (0.446%), neg=0, invalid=762 0059: dt=76.646707, rms=0.669 (0.366%), neg=0, invalid=762 0060: dt=76.646707, rms=0.666 (0.310%), neg=0, invalid=762 0061: dt=76.646707, rms=0.665 (0.260%), neg=0, invalid=762 0062: dt=76.646707, rms=0.663 (0.224%), neg=0, invalid=762 0063: dt=76.646707, rms=0.662 (0.206%), neg=0, invalid=762 0064: dt=76.646707, rms=0.661 (0.170%), neg=0, invalid=762 0065: dt=76.646707, rms=0.660 (0.151%), neg=0, invalid=762 0066: dt=76.646707, rms=0.659 (0.116%), neg=0, invalid=762 0067: dt=76.646707, rms=0.658 (0.134%), neg=0, invalid=762 0068: dt=76.646707, rms=0.657 (0.115%), neg=0, invalid=762 0069: dt=76.646707, rms=0.657 (0.103%), neg=0, invalid=762 0070: dt=9.072000, rms=0.657 (0.002%), neg=0, invalid=762 0071: dt=9.072000, rms=0.657 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.658, neg=0, invalid=762 0072: dt=82.944000, rms=0.656 (0.233%), neg=0, invalid=762 0073: dt=36.288000, rms=0.656 (0.008%), neg=0, invalid=762 0074: dt=36.288000, rms=0.656 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0075: dt=0.000000, rms=0.684 (0.130%), neg=0, invalid=762 0076: dt=0.000000, rms=0.684 (0.000%), neg=0, invalid=762 0077: dt=0.250000, rms=0.684 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0078: dt=0.000000, rms=0.684 (0.130%), neg=0, invalid=762 0079: dt=0.000000, rms=0.684 (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=0.767, neg=0, invalid=762 0080: dt=5.076923, rms=0.743 (3.174%), neg=0, invalid=762 0081: dt=2.635514, rms=0.741 (0.188%), neg=0, invalid=762 0082: dt=2.635514, rms=0.741 (-0.044%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.742, neg=0, invalid=762 0083: dt=0.009000, rms=0.741 (0.105%), neg=0, invalid=762 0084: dt=0.000000, rms=0.741 (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=0.817, neg=0, invalid=762 0085: dt=1.536000, rms=0.809 (0.934%), neg=0, invalid=762 0086: dt=2.086486, rms=0.802 (0.900%), neg=0, invalid=762 0087: dt=0.448000, rms=0.802 (0.059%), neg=0, invalid=762 0088: dt=0.448000, rms=0.801 (0.048%), neg=0, invalid=762 0089: dt=0.448000, rms=0.801 (0.054%), neg=0, invalid=762 0090: dt=0.448000, rms=0.801 (0.036%), neg=0, invalid=762 0091: dt=0.448000, rms=0.801 (0.003%), neg=0, invalid=762 0092: dt=1.792000, rms=0.799 (0.214%), neg=0, invalid=762 0093: dt=0.064000, rms=0.799 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.800, neg=0, invalid=762 0094: dt=1.024000, rms=0.798 (0.183%), neg=0, invalid=762 0095: dt=1.280000, rms=0.798 (0.042%), neg=0, invalid=762 0096: dt=1.280000, rms=0.798 (0.005%), neg=0, invalid=762 0097: dt=1.280000, rms=0.798 (-0.050%), 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=0.769, neg=0, invalid=762 0098: dt=1.046823, rms=0.740 (3.813%), neg=0, invalid=762 0099: dt=0.096000, rms=0.739 (0.182%), neg=0, invalid=762 0100: dt=0.096000, rms=0.739 (-0.100%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.739, neg=0, invalid=762 0101: dt=0.028000, rms=0.738 (0.117%), neg=0, invalid=762 0102: dt=0.007000, rms=0.738 (0.001%), neg=0, invalid=762 0103: dt=0.007000, rms=0.738 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.20493 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (162 voxels, overlap=0.004) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (162 voxels, peak = 6), gca=8.0 gca peak = 0.15565 (16) mri peak = 0.16618 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (185 voxels, overlap=0.023) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (185 voxels, peak = 5), gca=6.4 gca peak = 0.26829 (96) mri peak = 0.11390 (91) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (984 voxels, overlap=0.980) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (984 voxels, peak = 91), gca=90.7 gca peak = 0.20183 (93) mri peak = 0.09842 (92) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (834 voxels, overlap=1.001) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (834 voxels, peak = 91), gca=90.7 gca peak = 0.21683 (55) mri peak = 0.21253 (50) Right_Hippocampus: unreasonable value (48.7/50.0), not in range [50, 90] - rejecting gca peak = 0.30730 (58) mri peak = 0.14916 (50) Left_Hippocampus (17): linear fit = 0.87 x + 0.0 (853 voxels, overlap=0.415) Left_Hippocampus (17): linear fit = 0.87 x + 0.0 (853 voxels, peak = 50), gca=50.2 gca peak = 0.11430 (101) mri peak = 0.09607 (104) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (65602 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (65602 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.12221 (104) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (63970 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (63970 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.05353 (46) Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (19960 voxels, overlap=0.225) Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (19960 voxels, peak = 45), gca=45.1 gca peak = 0.15082 (58) mri peak = 0.06172 (45) Right_Cerebral_Cortex (42): linear fit = 0.76 x + 0.0 (20828 voxels, overlap=0.045) Right_Cerebral_Cortex (42): linear fit = 0.76 x + 0.0 (20828 voxels, peak = 44), gca=44.4 gca peak = 0.14161 (67) mri peak = 0.08882 (59) Right_Caudate (50): linear fit = 0.85 x + 0.0 (632 voxels, overlap=0.378) Right_Caudate (50): linear fit = 0.85 x + 0.0 (632 voxels, peak = 57), gca=56.6 gca peak = 0.15243 (71) mri peak = 0.09116 (65) Left_Caudate (11): linear fit = 0.86 x + 0.0 (1083 voxels, overlap=0.141) Left_Caudate (11): linear fit = 0.86 x + 0.0 (1083 voxels, peak = 61), gca=60.7 gca peak = 0.13336 (57) mri peak = 0.04756 (42) Left_Cerebellum_Cortex (8): linear fit = 0.80 x + 0.0 (24240 voxels, overlap=0.191) Left_Cerebellum_Cortex (8): linear fit = 0.80 x + 0.0 (24240 voxels, peak = 45), gca=45.3 gca peak = 0.13252 (56) mri peak = 0.05022 (46) Right_Cerebellum_Cortex (47): linear fit = 0.80 x + 0.0 (27356 voxels, overlap=0.114) Right_Cerebellum_Cortex (47): linear fit = 0.80 x + 0.0 (27356 voxels, peak = 45), gca=44.5 gca peak = 0.18181 (84) mri peak = 0.10300 (77) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (8375 voxels, overlap=0.578) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (8375 voxels, peak = 78), gca=77.7 gca peak = 0.20573 (83) mri peak = 0.10176 (82) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7705 voxels, overlap=0.978) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7705 voxels, peak = 82), gca=81.8 gca peak = 0.21969 (57) mri peak = 0.13103 (52) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (462 voxels, overlap=0.777) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (462 voxels, peak = 51), gca=51.0 gca peak = 0.39313 (56) mri peak = 0.28846 (50) Right_Amygdala: unreasonable value (49.6/50.0), not in range [50, 90] - rejecting gca peak = 0.14181 (85) mri peak = 0.06463 (86) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5711 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5711 voxels, peak = 85), gca=84.6 gca peak = 0.11978 (83) mri peak = 0.05721 (89) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4693 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4693 voxels, peak = 88), gca=87.6 gca peak = 0.13399 (79) mri peak = 0.07385 (73) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2572 voxels, overlap=0.619) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2572 voxels, peak = 74), gca=73.9 gca peak = 0.14159 (79) mri peak = 0.10978 (71) Right_Putamen (51): linear fit = 0.92 x + 0.0 (2502 voxels, overlap=0.444) Right_Putamen (51): linear fit = 0.92 x + 0.0 (2502 voxels, peak = 72), gca=72.3 gca peak = 0.10025 (80) mri peak = 0.11605 (84) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13796 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13796 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07013 (98) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1435 voxels, overlap=0.400) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1435 voxels, peak = 96), gca=95.9 gca peak = 0.12801 (89) mri peak = 0.07262 (89) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1692 voxels, overlap=0.623) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1692 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) mri peak = 0.22227 (13) gca peak = 0.15061 (21) mri peak = 0.09522 ( 5) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (202 voxels, overlap=0.403) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (202 voxels, peak = 8), gca=8.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) 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_Hippocampus = 0.21683 (55) gca peak Right_Amygdala = 0.39313 (56) 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 setting label Right_Hippocampus based on Left_Hippocampus = 0.87 x + 0: 50 setting label Right_Amygdala based on Left_Amygdala = 0.89 x + 0: 51 estimating mean gm scale to be 0.84 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 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=0.753, neg=0, invalid=762 0104: dt=129.472000, rms=0.748 (0.658%), neg=0, invalid=762 0105: dt=369.920000, rms=0.745 (0.392%), neg=0, invalid=762 0106: dt=129.472000, rms=0.744 (0.115%), neg=0, invalid=762 0107: dt=443.904000, rms=0.742 (0.347%), neg=0, invalid=762 0108: dt=73.984000, rms=0.741 (0.115%), neg=0, invalid=762 0109: dt=1479.680000, rms=0.738 (0.352%), neg=0, invalid=762 0110: dt=129.472000, rms=0.736 (0.375%), neg=0, invalid=762 0111: dt=73.984000, rms=0.735 (0.043%), neg=0, invalid=762 0112: dt=73.984000, rms=0.735 (0.035%), neg=0, invalid=762 0113: dt=73.984000, rms=0.735 (0.062%), neg=0, invalid=762 0114: dt=73.984000, rms=0.734 (0.085%), neg=0, invalid=762 0115: dt=73.984000, rms=0.733 (0.099%), neg=0, invalid=762 0116: dt=73.984000, rms=0.732 (0.104%), neg=0, invalid=762 0117: dt=73.984000, rms=0.732 (0.103%), neg=0, invalid=762 0118: dt=73.984000, rms=0.731 (0.094%), neg=0, invalid=762 0119: dt=73.984000, rms=0.730 (0.087%), neg=0, invalid=762 0120: dt=73.984000, rms=0.730 (0.079%), neg=0, invalid=762 0121: dt=73.984000, rms=0.729 (0.076%), neg=0, invalid=762 0122: dt=73.984000, rms=0.729 (0.072%), neg=0, invalid=762 0123: dt=73.984000, rms=0.728 (0.069%), neg=0, invalid=762 0124: dt=73.984000, rms=0.728 (0.070%), neg=0, invalid=762 0125: dt=73.984000, rms=0.727 (0.067%), neg=0, invalid=762 0126: dt=73.984000, rms=0.727 (0.062%), neg=0, invalid=762 0127: dt=73.984000, rms=0.726 (0.058%), neg=0, invalid=762 0128: dt=73.984000, rms=0.726 (0.055%), neg=0, invalid=762 0129: dt=73.984000, rms=0.726 (0.052%), neg=0, invalid=762 0130: dt=73.984000, rms=0.725 (0.048%), neg=0, invalid=762 0131: dt=73.984000, rms=0.725 (0.045%), neg=0, invalid=762 0132: dt=73.984000, rms=0.725 (0.040%), neg=0, invalid=762 0133: dt=73.984000, rms=0.724 (0.040%), neg=0, invalid=762 0134: dt=73.984000, rms=0.724 (0.038%), neg=0, invalid=762 0135: dt=73.984000, rms=0.724 (0.038%), neg=0, invalid=762 0136: dt=73.984000, rms=0.723 (0.038%), neg=0, invalid=762 0137: dt=73.984000, rms=0.723 (0.040%), neg=0, invalid=762 0138: dt=73.984000, rms=0.723 (0.039%), neg=0, invalid=762 0139: dt=73.984000, rms=0.723 (0.039%), neg=0, invalid=762 0140: dt=73.984000, rms=0.722 (0.039%), neg=0, invalid=762 0141: dt=73.984000, rms=0.722 (0.037%), neg=0, invalid=762 0142: dt=73.984000, rms=0.722 (0.035%), neg=0, invalid=762 0143: dt=73.984000, rms=0.722 (0.031%), neg=0, invalid=762 0144: dt=73.984000, rms=0.721 (0.032%), neg=0, invalid=762 0145: dt=73.984000, rms=0.721 (0.032%), neg=0, invalid=762 0146: dt=73.984000, rms=0.721 (0.031%), neg=0, invalid=762 0147: dt=73.984000, rms=0.721 (0.029%), neg=0, invalid=762 0148: dt=73.984000, rms=0.720 (0.028%), neg=0, invalid=762 0149: dt=73.984000, rms=0.720 (0.028%), neg=0, invalid=762 0150: dt=73.984000, rms=0.720 (0.026%), neg=0, invalid=762 0151: dt=73.984000, rms=0.720 (0.024%), neg=0, invalid=762 0152: dt=73.984000, rms=0.720 (0.024%), neg=0, invalid=762 0153: dt=2071.552000, rms=0.719 (0.048%), neg=0, invalid=762 0154: dt=55.488000, rms=0.719 (0.008%), neg=0, invalid=762 0155: dt=55.488000, rms=0.719 (0.005%), neg=0, invalid=762 0156: dt=55.488000, rms=0.719 (0.001%), neg=0, invalid=762 0157: dt=55.488000, rms=0.719 (0.003%), neg=0, invalid=762 0158: dt=55.488000, rms=0.719 (0.007%), neg=0, invalid=762 0159: dt=55.488000, rms=0.719 (0.010%), neg=0, invalid=762 0160: dt=55.488000, rms=0.719 (0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.720, neg=0, invalid=762 0161: dt=129.472000, rms=0.719 (0.169%), neg=0, invalid=762 0162: dt=443.904000, rms=0.718 (0.077%), neg=0, invalid=762 0163: dt=92.480000, rms=0.718 (0.018%), neg=0, invalid=762 0164: dt=92.480000, rms=0.718 (0.015%), neg=0, invalid=762 0165: dt=92.480000, rms=0.718 (0.020%), neg=0, invalid=762 0166: dt=92.480000, rms=0.718 (0.024%), neg=0, invalid=762 0167: dt=92.480000, rms=0.717 (0.025%), neg=0, invalid=762 0168: dt=92.480000, rms=0.717 (0.025%), neg=0, invalid=762 0169: dt=92.480000, rms=0.717 (0.027%), neg=0, invalid=762 0170: dt=92.480000, rms=0.717 (0.029%), neg=0, invalid=762 0171: dt=92.480000, rms=0.717 (0.031%), neg=0, invalid=762 0172: dt=92.480000, rms=0.716 (0.028%), neg=0, invalid=762 0173: dt=92.480000, rms=0.716 (0.025%), neg=0, invalid=762 0174: dt=92.480000, rms=0.716 (0.024%), neg=0, invalid=762 0175: dt=92.480000, rms=0.716 (0.021%), neg=0, invalid=762 0176: dt=517.888000, rms=0.716 (0.007%), neg=0, invalid=762 0177: dt=517.888000, rms=0.716 (0.030%), neg=0, invalid=762 0178: dt=517.888000, rms=0.716 (-0.015%), neg=0, invalid=762 0179: dt=27.744000, rms=0.716 (0.000%), neg=0, invalid=762 0180: dt=18.496000, rms=0.716 (-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=0.717, neg=0, invalid=762 0181: dt=276.810005, rms=0.705 (1.670%), neg=0, invalid=762 0182: dt=121.841924, rms=0.697 (1.175%), neg=0, invalid=762 0183: dt=79.238095, rms=0.694 (0.420%), neg=0, invalid=762 0184: dt=94.701671, rms=0.690 (0.564%), neg=0, invalid=762 0185: dt=36.288000, rms=0.688 (0.253%), neg=0, invalid=762 0186: dt=580.608000, rms=0.680 (1.178%), neg=0, invalid=762 0187: dt=65.269841, rms=0.673 (1.034%), neg=0, invalid=762 0188: dt=36.288000, rms=0.672 (0.186%), neg=0, invalid=762 0189: dt=497.664000, rms=0.667 (0.650%), neg=0, invalid=762 0190: dt=9.072000, rms=0.667 (0.139%), neg=0, invalid=762 0191: dt=7.776000, rms=0.666 (0.094%), neg=0, invalid=762 0192: dt=0.405000, rms=0.666 (0.003%), neg=0, invalid=762 0193: dt=0.025312, rms=0.666 (0.000%), neg=0, invalid=762 0194: dt=0.001582, rms=0.666 (0.000%), neg=0, invalid=762 0195: dt=0.000396, rms=0.666 (0.000%), neg=0, invalid=762 0196: dt=0.000000, rms=0.666 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=762 0197: dt=0.000000, rms=0.666 (0.157%), neg=0, invalid=762 0198: dt=0.000000, rms=0.666 (0.000%), neg=0, invalid=762 0199: dt=0.000439, rms=0.666 (0.000%), neg=0, invalid=762 0200: dt=0.000220, rms=0.666 (0.000%), neg=0, invalid=762 0201: dt=0.000110, 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=0.671, neg=0, invalid=762 0202: dt=0.000000, rms=0.670 (0.155%), neg=0, invalid=762 0203: dt=0.000000, rms=0.670 (0.000%), neg=0, invalid=762 0204: dt=0.000004, rms=0.670 (0.000%), neg=0, invalid=762 0205: dt=0.000000, rms=0.670 (0.000%), neg=0, invalid=762 0206: dt=0.000000, rms=0.670 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.671, neg=0, invalid=762 0207: dt=0.000000, rms=0.670 (0.155%), neg=0, invalid=762 0208: dt=0.000000, rms=0.670 (0.000%), neg=0, invalid=762 0209: dt=0.000000, rms=0.670 (0.000%), neg=0, invalid=762 0210: dt=0.000000, rms=0.670 (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=0.684, neg=0, invalid=762 0211: dt=0.000000, rms=0.683 (0.149%), neg=0, invalid=762 0212: dt=0.000000, rms=0.683 (0.000%), neg=0, invalid=762 0213: dt=0.000000, rms=0.683 (0.000%), neg=0, invalid=762 0214: dt=0.000000, rms=0.683 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0215: dt=0.000000, rms=0.683 (0.149%), neg=0, invalid=762 0216: dt=0.000000, rms=0.683 (0.000%), neg=0, invalid=762 0217: dt=0.000000, rms=0.683 (0.000%), neg=0, invalid=762 0218: dt=0.000000, rms=0.683 (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=0.711, neg=0, invalid=762 0219: dt=1.792000, rms=0.688 (3.256%), neg=0, invalid=762 0220: dt=6.144000, rms=0.650 (5.437%), neg=0, invalid=762 0221: dt=0.000000, rms=0.650 (0.004%), neg=0, invalid=762 0222: dt=0.100000, rms=0.650 (-0.034%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0223: dt=0.000000, rms=0.650 (0.153%), neg=0, invalid=762 0224: dt=0.000000, rms=0.650 (0.000%), neg=0, invalid=762 0225: dt=0.100000, rms=0.650 (-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=0.609, neg=0, invalid=762 0226: dt=0.448000, rms=0.586 (3.714%), neg=0, invalid=762 0227: dt=0.384000, rms=0.580 (0.980%), neg=0, invalid=762 0228: dt=0.448000, rms=0.576 (0.696%), neg=0, invalid=762 0229: dt=0.448000, rms=0.574 (0.395%), neg=0, invalid=762 0230: dt=0.448000, rms=0.572 (0.298%), neg=0, invalid=762 0231: dt=0.448000, rms=0.571 (0.202%), neg=0, invalid=762 0232: dt=0.448000, rms=0.570 (0.184%), neg=0, invalid=762 0233: dt=0.448000, rms=0.569 (0.126%), neg=0, invalid=762 0234: dt=0.448000, rms=0.569 (0.124%), neg=0, invalid=762 0235: dt=0.448000, rms=0.568 (0.087%), neg=0, invalid=762 0236: dt=0.448000, rms=0.568 (0.092%), neg=0, invalid=762 0237: dt=0.448000, rms=0.567 (0.061%), neg=0, invalid=762 0238: dt=0.448000, rms=0.567 (0.072%), neg=0, invalid=762 0239: dt=0.448000, rms=0.567 (0.044%), neg=0, invalid=762 0240: dt=0.448000, rms=0.566 (0.059%), neg=0, invalid=762 0241: dt=0.448000, rms=0.566 (0.083%), neg=0, invalid=762 0242: dt=0.224000, rms=0.566 (0.020%), neg=0, invalid=762 0243: dt=0.224000, rms=0.566 (0.033%), neg=0, invalid=762 0244: dt=0.224000, rms=0.565 (0.044%), neg=0, invalid=762 0245: dt=0.224000, rms=0.565 (0.042%), neg=0, invalid=762 0246: dt=0.224000, rms=0.565 (0.048%), neg=0, invalid=762 0247: dt=0.224000, rms=0.564 (0.057%), neg=0, invalid=762 0248: dt=0.224000, rms=0.564 (0.057%), neg=0, invalid=762 0249: dt=0.224000, rms=0.564 (0.052%), neg=0, invalid=762 0250: dt=0.224000, rms=0.564 (0.004%), neg=0, invalid=762 0251: dt=0.224000, rms=0.564 (0.006%), neg=0, invalid=762 0252: dt=0.224000, rms=0.564 (0.009%), neg=0, invalid=762 0253: dt=0.224000, rms=0.564 (0.014%), neg=0, invalid=762 0254: dt=0.224000, rms=0.564 (0.003%), neg=0, invalid=762 0255: dt=0.112000, rms=0.564 (0.002%), neg=0, invalid=762 0256: dt=0.112000, rms=0.564 (0.003%), neg=0, invalid=762 0257: dt=0.112000, rms=0.564 (0.003%), neg=0, invalid=762 0258: dt=0.112000, rms=0.564 (0.002%), neg=0, invalid=762 0259: dt=0.112000, rms=0.564 (0.004%), neg=0, invalid=762 0260: dt=0.112000, rms=0.564 (0.008%), neg=0, invalid=762 0261: dt=0.112000, rms=0.564 (0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=762 0262: dt=0.320000, rms=0.559 (0.920%), neg=0, invalid=762 0263: dt=0.112000, rms=0.559 (0.092%), neg=0, invalid=762 0264: dt=0.384000, rms=0.558 (0.239%), neg=0, invalid=762 0265: dt=0.384000, rms=0.557 (0.051%), neg=0, invalid=762 0266: dt=0.384000, rms=0.557 (0.012%), neg=0, invalid=762 0267: dt=0.384000, rms=0.557 (-0.008%), 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=0.555, neg=0, invalid=762 0268: dt=27.744000, rms=0.554 (0.206%), neg=0, invalid=762 0269: dt=5.780000, rms=0.554 (0.001%), neg=0, invalid=762 0270: dt=5.780000, rms=0.554 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=762 0271: dt=73.984000, rms=0.554 (0.234%), neg=0, invalid=762 0272: dt=129.472000, rms=0.554 (0.032%), neg=0, invalid=762 0273: dt=129.472000, rms=0.554 (0.018%), neg=0, invalid=762 0274: dt=129.472000, rms=0.554 (0.031%), neg=0, invalid=762 0275: dt=129.472000, rms=0.554 (0.016%), neg=0, invalid=762 0276: dt=129.472000, rms=0.553 (0.023%), neg=0, invalid=762 0277: dt=129.472000, rms=0.553 (0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.554, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0278: dt=77.543568, rms=0.552 (0.476%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0279: dt=103.680000, rms=0.550 (0.248%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0280: dt=103.680000, rms=0.550 (-0.125%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0281: dt=64.748538, rms=0.549 (0.556%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0282: dt=36.288000, rms=0.548 (0.145%), neg=0, invalid=762 0283: dt=36.288000, rms=0.547 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0284: dt=36.288000, rms=0.547 (0.137%), neg=0, invalid=762 0285: dt=36.288000, rms=0.546 (0.185%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0286: dt=36.288000, rms=0.545 (0.151%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0287: dt=36.288000, rms=0.544 (0.179%), neg=0, invalid=762 0288: dt=36.288000, rms=0.543 (0.131%), neg=0, invalid=762 0289: dt=36.288000, rms=0.542 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0290: dt=36.288000, rms=0.542 (0.105%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0291: dt=36.288000, rms=0.541 (0.098%), neg=0, invalid=762 0292: dt=36.288000, rms=0.541 (0.033%), neg=0, invalid=762 0293: dt=36.288000, rms=0.541 (0.026%), neg=0, invalid=762 0294: dt=36.288000, rms=0.541 (0.038%), neg=0, invalid=762 0295: dt=36.288000, rms=0.540 (0.046%), neg=0, invalid=762 0296: dt=36.288000, rms=0.540 (0.047%), neg=0, invalid=762 0297: dt=36.288000, rms=0.540 (0.060%), neg=0, invalid=762 0298: dt=36.288000, rms=0.540 (0.055%), neg=0, invalid=762 0299: dt=36.288000, rms=0.539 (0.058%), neg=0, invalid=762 0300: dt=36.288000, rms=0.539 (0.057%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.541, neg=0, invalid=762 iter 0, gcam->neg = 15 after 10 iterations, nbhd size=1, neg = 0 0301: dt=53.250965, rms=0.534 (1.141%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0302: dt=66.681564, rms=0.529 (1.015%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0303: dt=21.229268, rms=0.527 (0.476%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 10 iterations, nbhd size=1, neg = 0 0304: dt=109.419355, rms=0.525 (0.275%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0305: dt=35.602094, rms=0.522 (0.625%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0306: dt=38.400000, rms=0.521 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0307: dt=38.400000, rms=0.520 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0308: dt=38.400000, rms=0.518 (0.317%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 11 iterations, nbhd size=1, neg = 0 0309: dt=38.400000, rms=0.517 (0.243%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0310: dt=38.400000, rms=0.515 (0.390%), neg=0, invalid=762 iter 0, gcam->neg = 26 after 10 iterations, nbhd size=1, neg = 0 0311: dt=38.400000, rms=0.513 (0.388%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 9 iterations, nbhd size=1, neg = 0 0312: dt=38.400000, rms=0.511 (0.320%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 12 iterations, nbhd size=1, neg = 0 0313: dt=38.400000, rms=0.510 (0.300%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 10 iterations, nbhd size=1, neg = 0 0314: dt=38.400000, rms=0.508 (0.273%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 13 iterations, nbhd size=1, neg = 0 0315: dt=38.400000, rms=0.507 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 10 iterations, nbhd size=1, neg = 0 0316: dt=38.400000, rms=0.506 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 13 iterations, nbhd size=1, neg = 0 0317: dt=38.400000, rms=0.506 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 6 iterations, nbhd size=0, neg = 0 0318: dt=38.400000, rms=0.505 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 14 iterations, nbhd size=1, neg = 0 0319: dt=38.400000, rms=0.504 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0320: dt=38.400000, rms=0.504 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=1, neg = 0 0321: dt=38.400000, rms=0.503 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 4 iterations, nbhd size=0, neg = 0 0322: dt=38.400000, rms=0.503 (0.027%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0323: dt=38.400000, rms=0.503 (0.063%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0324: dt=38.400000, rms=0.502 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0325: dt=38.400000, rms=0.502 (0.068%), neg=0, invalid=762 0326: dt=11.200000, rms=0.501 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0327: dt=11.200000, rms=0.501 (0.018%), neg=0, invalid=762 0328: dt=11.200000, rms=0.501 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0329: dt=11.200000, rms=0.501 (0.019%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0330: dt=11.200000, rms=0.501 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0331: dt=11.200000, rms=0.501 (0.022%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0332: dt=44.800000, rms=0.498 (0.873%), neg=0, invalid=762 0333: dt=38.400000, rms=0.497 (0.224%), neg=0, invalid=762 0334: dt=38.400000, rms=0.497 (-0.118%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0335: dt=1.008000, rms=0.510 (0.215%), neg=0, invalid=762 0336: dt=0.864000, rms=0.510 (0.001%), neg=0, invalid=762 0337: dt=0.864000, rms=0.510 (0.000%), neg=0, invalid=762 0338: dt=0.864000, rms=0.510 (-0.027%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0339: dt=2.844444, rms=0.510 (0.269%), neg=0, invalid=762 0340: dt=1.500000, rms=0.510 (0.011%), neg=0, invalid=762 0341: dt=1.500000, rms=0.510 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.531, neg=0, invalid=762 0342: dt=1.024000, rms=0.528 (0.492%), neg=0, invalid=762 0343: dt=0.448000, rms=0.528 (0.031%), neg=0, invalid=762 0344: dt=0.448000, rms=0.528 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.529, neg=0, invalid=762 0345: dt=1.024000, rms=0.527 (0.351%), neg=0, invalid=762 0346: dt=0.448000, rms=0.527 (0.028%), neg=0, invalid=762 0347: dt=0.448000, rms=0.527 (0.013%), neg=0, invalid=762 0348: dt=0.448000, rms=0.527 (-0.028%), 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=0.511, neg=0, invalid=762 iter 0, gcam->neg = 2053 after 17 iterations, nbhd size=1, neg = 0 0349: dt=2.561433, rms=0.471 (7.869%), neg=0, invalid=762 0350: dt=0.127273, rms=0.469 (0.311%), neg=0, invalid=762 0351: dt=0.080000, rms=0.469 (0.056%), neg=0, invalid=762 0352: dt=0.080000, rms=0.469 (-0.037%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0353: dt=0.096000, rms=0.469 (0.376%), neg=0, invalid=762 0354: dt=0.007000, rms=0.469 (0.001%), neg=0, invalid=762 0355: dt=0.007000, rms=0.469 (0.000%), neg=0, invalid=762 0356: dt=0.007000, rms=0.469 (-0.001%), 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=0.452, neg=0, invalid=762 0357: dt=0.000000, rms=0.452 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0358: dt=73.984000, rms=0.452 (0.015%), neg=0, invalid=762 0359: dt=129.472000, rms=0.452 (0.008%), neg=0, invalid=762 0360: dt=129.472000, rms=0.452 (0.001%), neg=0, invalid=762 0361: dt=129.472000, rms=0.452 (0.006%), neg=0, invalid=762 0362: dt=129.472000, rms=0.452 (0.005%), neg=0, invalid=762 0363: dt=129.472000, rms=0.452 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0364: dt=9.072000, rms=0.452 (0.005%), neg=0, invalid=762 0365: dt=0.567000, rms=0.452 (0.000%), neg=0, invalid=762 0366: dt=0.567000, rms=0.452 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0367: dt=145.152000, rms=0.452 (0.102%), neg=0, invalid=762 0368: dt=62.208000, rms=0.451 (0.062%), neg=0, invalid=762 0369: dt=62.208000, rms=0.451 (0.009%), neg=0, invalid=762 0370: dt=62.208000, rms=0.451 (0.028%), neg=0, invalid=762 0371: dt=62.208000, rms=0.451 (0.055%), neg=0, invalid=762 0372: dt=62.208000, rms=0.451 (0.029%), neg=0, invalid=762 0373: dt=62.208000, rms=0.451 (0.014%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0374: dt=21.246964, rms=0.451 (0.209%), neg=0, invalid=762 0375: dt=38.400000, rms=0.450 (0.169%), neg=0, invalid=762 0376: dt=38.400000, rms=0.449 (0.165%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=1, neg = 0 0377: dt=38.400000, rms=0.449 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 11 iterations, nbhd size=1, neg = 0 0378: dt=38.400000, rms=0.449 (-0.019%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 11 iterations, nbhd size=1, neg = 0 0379: dt=153.600000, rms=0.447 (0.262%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0380: dt=11.200000, rms=0.447 (0.060%), neg=0, invalid=762 0381: dt=11.200000, rms=0.447 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0382: dt=11.200000, rms=0.447 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0383: dt=11.200000, rms=0.447 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0384: dt=11.200000, rms=0.447 (0.024%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0385: dt=11.200000, rms=0.447 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0386: dt=11.200000, rms=0.446 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=0, neg = 0 0387: dt=11.200000, rms=0.446 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0388: dt=44.800000, rms=0.446 (0.032%), 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 = 3 after 1 iterations, nbhd size=0, neg = 0 0389: dt=43.246377, rms=0.443 (0.777%), neg=0, invalid=762 0390: dt=32.000000, rms=0.441 (0.296%), neg=0, invalid=762 0391: dt=25.600000, rms=0.441 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0392: dt=25.600000, rms=0.440 (0.107%), neg=0, invalid=762 0393: dt=25.600000, rms=0.440 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0394: dt=25.600000, rms=0.439 (0.154%), neg=0, invalid=762 0395: dt=25.600000, rms=0.438 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0396: dt=25.600000, rms=0.438 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0397: dt=25.600000, rms=0.437 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0398: dt=25.600000, rms=0.437 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0399: dt=44.800000, rms=0.437 (0.045%), neg=0, invalid=762 0400: dt=44.800000, rms=0.436 (0.045%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0401: dt=44.800000, rms=0.436 (0.057%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0402: dt=44.800000, rms=0.436 (0.058%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0403: dt=44.800000, rms=0.436 (0.075%), neg=0, invalid=762 0404: dt=44.800000, rms=0.435 (0.074%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0405: dt=44.800000, rms=0.435 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0406: dt=44.800000, rms=0.434 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0407: dt=44.800000, rms=0.434 (0.087%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.440, neg=0, invalid=762 0408: dt=0.000246, rms=0.440 (0.000%), neg=0, invalid=762 0409: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=762 0410: dt=0.000000, rms=0.440 (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=0.451, neg=0, invalid=762 0411: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0412: dt=0.256000, rms=0.451 (0.014%), neg=0, invalid=762 0413: dt=0.048000, rms=0.451 (0.000%), neg=0, invalid=762 0414: dt=0.048000, 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=0.433, neg=0, invalid=762 iter 0, gcam->neg = 1139 after 13 iterations, nbhd size=1, neg = 0 0415: dt=1.553985, rms=0.418 (3.357%), neg=0, invalid=762 0416: dt=0.000013, rms=0.418 (0.000%), neg=0, invalid=762 0417: dt=0.000013, rms=0.418 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0418: dt=0.080000, rms=0.418 (0.049%), neg=0, invalid=762 0419: dt=0.020000, rms=0.418 (0.003%), neg=0, invalid=762 0420: dt=0.020000, rms=0.418 (-0.001%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 48 minutes and 38 seconds. mri_ca_register utimesec 18527.628000 mri_ca_register stimesec 283.224000 mri_ca_register ru_maxrss 1338924 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 103791659 mri_ca_register ru_majflt 3 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 464 mri_ca_register ru_oublock 63136 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 840620 mri_ca_register ru_nivcsw 2228584 FSRUNTIME@ mri_ca_register 2.8104 hours 64 threads #-------------------------------------- #@# SubCort Seg Tue Jul 23 02:06:07 EDT 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname roxy machine x86_64 setenv SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 cd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 64 == 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 /opt/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 7.00 Atlas used for the 3D morph was /opt/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 = 0.19571 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.09 x + 0.0 (701 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (701 voxels, peak = 2), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.17555 ( 2) Right_Lateral_Ventricle (43): linear fit = 0.08 x + 0.0 (675 voxels, overlap=0.005) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (675 voxels, peak = 1), gca=5.2 gca peak = 0.28129 (95) mri peak = 0.11630 (96) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (768 voxels, overlap=1.012) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (768 voxels, peak = 90), gca=89.8 gca peak = 0.16930 (96) mri peak = 0.11112 (95) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (761 voxels, overlap=1.005) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (761 voxels, peak = 95), gca=94.6 gca peak = 0.24553 (55) mri peak = 0.28796 (50) Right_Hippocampus: unreasonable value (48.7/50.0), not in range [50, 90] - rejecting gca peak = 0.30264 (59) mri peak = 0.15641 (50) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (990 voxels, overlap=0.892) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (990 voxels, peak = 52), gca=51.6 gca peak = 0.07580 (103) mri peak = 0.09970 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (52273 voxels, overlap=0.640) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (52273 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.12227 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54548 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54548 voxels, peak = 104), gca=104.0 gca peak = 0.09712 (58) mri peak = 0.06106 (42) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (26177 voxels, overlap=0.375) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (26177 voxels, peak = 46), gca=46.1 gca peak = 0.11620 (58) mri peak = 0.05883 (47) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (24108 voxels, overlap=0.261) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (24108 voxels, peak = 46), gca=46.1 gca peak = 0.30970 (66) mri peak = 0.09728 (59) Right_Caudate (50): linear fit = 0.87 x + 0.0 (1403 voxels, overlap=0.116) Right_Caudate (50): linear fit = 0.87 x + 0.0 (1403 voxels, peak = 57), gca=57.1 gca peak = 0.15280 (69) mri peak = 0.09848 (65) Left_Caudate (11): linear fit = 0.86 x + 0.0 (1275 voxels, overlap=0.247) Left_Caudate (11): linear fit = 0.86 x + 0.0 (1275 voxels, peak = 59), gca=59.0 gca peak = 0.13902 (56) mri peak = 0.04829 (42) Left_Cerebellum_Cortex (8): linear fit = 0.79 x + 0.0 (23828 voxels, overlap=0.137) Left_Cerebellum_Cortex (8): linear fit = 0.79 x + 0.0 (23828 voxels, peak = 44), gca=44.0 gca peak = 0.14777 (55) mri peak = 0.05267 (46) Right_Cerebellum_Cortex (47): linear fit = 0.80 x + 0.0 (24754 voxels, overlap=0.117) Right_Cerebellum_Cortex (47): linear fit = 0.80 x + 0.0 (24754 voxels, peak = 44), gca=43.7 gca peak = 0.16765 (84) mri peak = 0.11415 (77) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (6289 voxels, overlap=0.595) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (6289 voxels, peak = 78), gca=77.7 gca peak = 0.18739 (84) mri peak = 0.12027 (82) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (6093 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (6093 voxels, peak = 82), gca=81.9 gca peak = 0.29869 (57) mri peak = 0.16279 (51) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (550 voxels, overlap=0.852) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (550 voxels, peak = 51), gca=51.0 gca peak = 0.33601 (57) mri peak = 0.22371 (51) Right_Amygdala: unreasonable value (49.9/51.0), not in range [50, 90] - rejecting gca peak = 0.11131 (90) mri peak = 0.08605 (86) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3743 voxels, overlap=1.000) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3743 voxels, peak = 87), gca=86.8 gca peak = 0.11793 (83) mri peak = 0.06854 (89) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3883 voxels, overlap=0.980) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3883 voxels, peak = 88), gca=87.6 gca peak = 0.08324 (81) mri peak = 0.08004 (73) Left_Putamen (12): linear fit = 0.92 x + 0.0 (2381 voxels, overlap=0.582) Left_Putamen (12): linear fit = 0.92 x + 0.0 (2381 voxels, peak = 74), gca=74.1 gca peak = 0.10360 (77) mri peak = 0.11478 (71) Right_Putamen (51): linear fit = 0.92 x + 0.0 (2334 voxels, overlap=0.690) Right_Putamen (51): linear fit = 0.92 x + 0.0 (2334 voxels, peak = 70), gca=70.5 gca peak = 0.08424 (78) mri peak = 0.11139 (84) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11051 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11051 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.08315 (98) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1461 voxels, overlap=0.482) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1461 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.07504 (89) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1540 voxels, overlap=0.795) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1540 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.16794 ( 2) gca peak = 0.19357 (14) mri peak = 0.11732 ( 2) Fourth_Ventricle (15): linear fit = 0.06 x + 0.0 (436 voxels, overlap=0.381) Fourth_Ventricle (15): linear fit = 0.06 x + 0.0 (436 voxels, peak = 1), gca=0.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) 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_Hippocampus = 0.24553 (55) gca peak Right_Amygdala = 0.33601 (57) 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 setting label Right_Hippocampus based on Left_Hippocampus = 0.88 x + 0: 52 setting label Right_Amygdala based on Left_Amygdala = 0.89 x + 0: 51 estimating mean gm scale to be 0.86 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30837 ( 7) mri peak = 0.19571 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (701 voxels, overlap=0.418) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (701 voxels, peak = 2), gca=2.8 gca peak = 0.30173 ( 5) mri peak = 0.17555 ( 2) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (675 voxels, overlap=0.669) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (675 voxels, peak = 1), gca=2.0 gca peak = 0.27103 (89) mri peak = 0.11630 (96) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (768 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (768 voxels, peak = 90), gca=90.3 gca peak = 0.18643 (95) mri peak = 0.11112 (95) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (761 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (761 voxels, peak = 95), gca=94.5 gca peak = 0.29611 (49) mri peak = 0.28796 (50) Right_Hippocampus: unreasonable value (49.7/50.0), not in range [50, 90] - rejecting gca peak = 0.32274 (52) mri peak = 0.15641 (50) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (990 voxels, overlap=0.986) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (990 voxels, peak = 52), gca=52.0 gca peak = 0.07767 (104) mri peak = 0.09970 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52273 voxels, overlap=0.705) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52273 voxels, peak = 103), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.12227 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54548 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54548 voxels, peak = 104), gca=104.0 gca peak = 0.12315 (46) mri peak = 0.06106 (42) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (26177 voxels, overlap=0.991) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (26177 voxels, peak = 45), gca=44.9 gca peak = 0.14785 (46) mri peak = 0.05883 (47) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (24108 voxels, overlap=0.979) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (24108 voxels, peak = 46), gca=46.0 gca peak = 0.29496 (57) mri peak = 0.09728 (59) Right_Caudate (50): linear fit = 1.02 x + 0.0 (1403 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.02 x + 0.0 (1403 voxels, peak = 58), gca=58.4 gca peak = 0.15014 (59) mri peak = 0.09848 (65) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1275 voxels, overlap=0.935) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1275 voxels, peak = 58), gca=58.1 gca peak = 0.18035 (43) mri peak = 0.04829 (42) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (23828 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (23828 voxels, peak = 45), gca=44.5 gca peak = 0.17885 (44) mri peak = 0.05267 (46) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (24754 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (24754 voxels, peak = 46), gca=45.5 gca peak = 0.17443 (78) mri peak = 0.11415 (77) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6289 voxels, overlap=0.951) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6289 voxels, peak = 79), gca=79.2 gca peak = 0.18538 (82) mri peak = 0.12027 (82) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6093 voxels, overlap=0.916) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6093 voxels, peak = 83), gca=83.2 gca peak = 0.29804 (51) mri peak = 0.16279 (51) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (550 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (550 voxels, peak = 51), gca=51.0 gca peak = 0.35151 (51) mri peak = 0.22371 (51) Right_Amygdala: unreasonable value (49.7/51.0), not in range [50, 90] - rejecting gca peak = 0.11053 (87) mri peak = 0.08605 (86) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3743 voxels, overlap=0.973) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3743 voxels, peak = 87), gca=86.6 gca peak = 0.10024 (85) mri peak = 0.06854 (89) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3883 voxels, overlap=0.999) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3883 voxels, peak = 86), gca=86.3 gca peak = 0.08998 (74) mri peak = 0.08004 (73) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2381 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2381 voxels, peak = 74), gca=74.0 gca peak = 0.11380 (69) mri peak = 0.11478 (71) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2334 voxels, overlap=0.986) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2334 voxels, peak = 70), gca=70.0 gca peak = 0.06682 (83) mri peak = 0.11139 (84) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11051 voxels, overlap=0.691) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11051 voxels, peak = 82), gca=81.8 gca peak = 0.11465 (92) mri peak = 0.08315 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1461 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1461 voxels, peak = 92), gca=91.5 gca peak = 0.16385 (91) mri peak = 0.07504 (89) Left_VentralDC (28): linear fit = 0.96 x + 0.0 (1540 voxels, overlap=0.921) Left_VentralDC (28): linear fit = 0.96 x + 0.0 (1540 voxels, peak = 88), gca=87.8 gca peak = 0.33708 (10) mri peak = 0.16794 ( 2) gca peak = 0.45928 ( 6) mri peak = 0.11732 ( 2) Fourth_Ventricle (15): linear fit = 0.16 x + 0.0 (436 voxels, overlap=0.982) Fourth_Ventricle (15): linear fit = 0.16 x + 0.0 (436 voxels, peak = 1), gca=0.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18368 (24) gca peak Left_Thalamus = 0.36646 (84) gca peak Third_Ventricle = 0.33708 (10) gca peak Fourth_Ventricle = 0.45928 ( 6) gca peak CSF = 0.26605 (13) gca peak Left_Accumbens_area = 0.81854 (53) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.71704 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.22401 (20) gca peak Right_Hippocampus = 0.29611 (49) gca peak Right_Amygdala = 0.35151 (51) gca peak Right_Accumbens_area = 0.32347 (56) gca peak Right_vessel = 0.71201 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65560 (13) gca peak WM_hypointensities = 0.07355 (77) gca peak non_WM_hypointensities = 0.09284 (44) gca peak Optic_Chiasm = 0.70643 (75) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 1.00 x + 0: 52 setting label Right_Amygdala based on Left_Amygdala = 1.00 x + 0: 51 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 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 70431 voxels changed in iteration 0 of unlikely voxel relabeling 156 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 25270 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 358 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 77762 changed. image ll: -2.160, PF=0.500 pass 2: 24925 changed. image ll: -2.160, PF=0.500 pass 3: 9532 changed. pass 4: 4303 changed. 45826 voxels changed in iteration 0 of unlikely voxel relabeling 291 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 6775 voxels changed in iteration 0 of unlikely voxel relabeling 74 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 5895 voxels changed in iteration 0 of unlikely voxel relabeling 58 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5350 voxels changed in iteration 0 of unlikely voxel relabeling 29 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 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 6510.328000 mri_ca_label stimesec 41.880000 mri_ca_label ru_maxrss 2133924 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 31105115 mri_ca_label ru_majflt 3 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 352 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 20509 mri_ca_label ru_nivcsw 560933 auto-labeling took 106 minutes and 42 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/transforms/cc_up.lta seg will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/transforms/cc_up.lta reading aseg from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aseg.auto_noCCseg.mgz reading norm from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/norm.mgz 28663 voxels in left wm, 31086 in right wm, xrange [121, 128] searching rotation angles z=[-5 9], y=[-5 9] searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.1 global minimum found at slice 124.1, rotations (1.96, 2.36) final transformation (x=124.1, yr=1.965, zr=2.359): 0.99856 -0.04117 0.03425 3.80949; 0.04114 0.99915 0.00141 27.80229; -0.03428 0.00000 0.99941 11.32681; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 95 121 eigenvectors: -0.00167 0.00421 0.99999; 0.01640 -0.99986 0.00423; 0.99986 0.01641 0.00160; writing aseg with callosum to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aseg.auto.mgz... corpus callosum segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Tue Jul 23 03:53:38 EDT 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Jul 23 03:53:38 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/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... 1030 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 110 gm peak at 53 (53), valley at 0 (-1) csf peak at 26, setting threshold to 44 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 51 (51), valley at 0 (-1) csf peak at 25, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 34 seconds. #-------------------------------------------- #@# Mask BFS Tue Jul 23 03:58:14 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1660849 voxels in mask (pct= 9.90) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Jul 23 03:58:15 EDT 2019 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 (107.0): 107.2 +- 5.0 [79.0 --> 125.0] GM (63.0) : 62.1 +- 11.2 [30.0 --> 95.0] setting bottom of white matter range to 73.3 setting top of gray matter range to 84.5 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... 6808 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6141 filled 813 bright non-wm voxels segmented. 3170 diagonally connected voxels added... white matter segmentation took 2.2 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 0.97 minutes reading wm segmentation from wm.seg.mgz... 483 voxels added to wm to prevent paths from MTL structures to cortex 3203 additional wm voxels added 0 additional wm voxels added SEG EDIT: 73597 voxels turned on, 43820 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 66 found - 66 modified | TOTAL: 66 pass 2 (xy+): 0 found - 66 modified | TOTAL: 66 pass 1 (xy-): 22 found - 22 modified | TOTAL: 88 pass 2 (xy-): 0 found - 22 modified | TOTAL: 88 pass 1 (yz+): 34 found - 34 modified | TOTAL: 122 pass 2 (yz+): 0 found - 34 modified | TOTAL: 122 pass 1 (yz-): 20 found - 20 modified | TOTAL: 142 pass 2 (yz-): 0 found - 20 modified | TOTAL: 142 pass 1 (xz+): 30 found - 30 modified | TOTAL: 172 pass 2 (xz+): 0 found - 30 modified | TOTAL: 172 pass 1 (xz-): 36 found - 36 modified | TOTAL: 208 pass 2 (xz-): 0 found - 36 modified | TOTAL: 208 Iteration Number : 1 pass 1 (+++): 19 found - 19 modified | TOTAL: 19 pass 2 (+++): 0 found - 19 modified | TOTAL: 19 pass 1 (+++): 30 found - 30 modified | TOTAL: 49 pass 2 (+++): 0 found - 30 modified | TOTAL: 49 pass 1 (+++): 28 found - 28 modified | TOTAL: 77 pass 2 (+++): 0 found - 28 modified | TOTAL: 77 pass 1 (+++): 26 found - 26 modified | TOTAL: 103 pass 2 (+++): 0 found - 26 modified | TOTAL: 103 Iteration Number : 1 pass 1 (++): 124 found - 124 modified | TOTAL: 124 pass 2 (++): 0 found - 124 modified | TOTAL: 124 pass 1 (+-): 173 found - 173 modified | TOTAL: 297 pass 2 (+-): 0 found - 173 modified | TOTAL: 297 pass 1 (--): 111 found - 111 modified | TOTAL: 408 pass 2 (--): 0 found - 111 modified | TOTAL: 408 pass 1 (-+): 214 found - 214 modified | TOTAL: 622 pass 2 (-+): 0 found - 214 modified | TOTAL: 622 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 5 found - 5 modified | TOTAL: 14 pass 2 (xy-): 0 found - 5 modified | TOTAL: 14 pass 1 (yz+): 8 found - 8 modified | TOTAL: 22 pass 2 (yz+): 0 found - 8 modified | TOTAL: 22 pass 1 (yz-): 10 found - 10 modified | TOTAL: 32 pass 2 (yz-): 0 found - 10 modified | TOTAL: 32 pass 1 (xz+): 6 found - 6 modified | TOTAL: 38 pass 2 (xz+): 0 found - 6 modified | TOTAL: 38 pass 1 (xz-): 9 found - 9 modified | TOTAL: 47 pass 2 (xz-): 0 found - 9 modified | TOTAL: 47 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 8 pass 2 (+++): 0 found - 6 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 1 found - 1 modified | TOTAL: 5 pass 2 (+-): 0 found - 1 modified | TOTAL: 5 pass 1 (--): 2 found - 2 modified | TOTAL: 7 pass 2 (--): 0 found - 2 modified | TOTAL: 7 pass 1 (-+): 13 found - 13 modified | TOTAL: 20 pass 2 (-+): 0 found - 13 modified | TOTAL: 20 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-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 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-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 = 1018 (out of 631510: 0.161201) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Jul 23 04:01:35 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/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 0.99146 -0.08331 0.04369 5.43546; 0.05799 1.11813 0.08084 -23.41093; -0.05135 -0.08063 1.01827 0.70063; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.99146 -0.08331 0.04369 5.43546; 0.05799 1.11813 0.08084 -23.41093; -0.05135 -0.08063 1.01827 0.70063; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1452 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) need search nearby using seed (126, 121, 150), TAL = (2.0, 22.0, 7.0) talairach voxel to voxel transform 1.00193 0.07115 -0.04864 -3.74625; -0.05530 0.88533 -0.06791 21.07461; 0.04615 0.07369 0.97422 0.79179; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 121, 150) --> (2.0, 22.0, 7.0) done. writing output to filled.mgz... filling took 1.1 minutes talairach cc position changed to (2.00, 22.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 22.00, 7.00) SRC: (105.78, 112.04, 160.83) search lh wm seed point around talairach space (-16.00, 22.00, 7.00), SRC: (141.85, 110.05, 162.49) 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 Tue Jul 23 04:02:41 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 2 found - 2 modified | TOTAL: 5 pass 2 (xz+): 0 found - 2 modified | TOTAL: 5 pass 1 (xz-): 1 found - 1 modified | TOTAL: 6 pass 2 (xz-): 0 found - 1 modified | TOTAL: 6 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 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 Iteration Number : 2 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+): 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 : 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 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 = 12 (out of 296568: 0.004046) 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 50: 2022 vertices, 2161 faces slice 60: 7854 vertices, 8144 faces slice 70: 16794 vertices, 17123 faces slice 80: 27001 vertices, 27365 faces slice 90: 38222 vertices, 38580 faces slice 100: 49635 vertices, 50021 faces slice 110: 61425 vertices, 61825 faces slice 120: 73620 vertices, 74007 faces slice 130: 85069 vertices, 85467 faces slice 140: 96471 vertices, 96860 faces slice 150: 107699 vertices, 108059 faces slice 160: 117227 vertices, 117540 faces slice 170: 124649 vertices, 124911 faces slice 180: 131921 vertices, 132185 faces slice 190: 138073 vertices, 138306 faces slice 200: 143441 vertices, 143617 faces slice 210: 145482 vertices, 145496 faces slice 220: 145482 vertices, 145496 faces slice 230: 145482 vertices, 145496 faces slice 240: 145482 vertices, 145496 faces slice 250: 145482 vertices, 145496 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... 145482 voxel in cpt #1: X=-14 [v=145482,e=436488,f=290992] located at (-26.234030, -7.922650, 23.565891) For the whole surface: X=-14 [v=145482,e=436488,f=290992] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Tue Jul 23 04:02:54 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 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+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 2 found - 2 modified | TOTAL: 5 pass 2 (yz-): 0 found - 2 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 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 (+-): 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 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 = 6 (out of 305217: 0.001966) 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 50: 1929 vertices, 2074 faces slice 60: 8938 vertices, 9212 faces slice 70: 18181 vertices, 18562 faces slice 80: 29595 vertices, 30014 faces slice 90: 40766 vertices, 41130 faces slice 100: 52404 vertices, 52813 faces slice 110: 65534 vertices, 65968 faces slice 120: 79235 vertices, 79748 faces slice 130: 93031 vertices, 93562 faces slice 140: 106611 vertices, 107119 faces slice 150: 118024 vertices, 118450 faces slice 160: 126790 vertices, 127118 faces slice 170: 134028 vertices, 134352 faces slice 180: 141324 vertices, 141644 faces slice 190: 147407 vertices, 147701 faces slice 200: 152115 vertices, 152304 faces slice 210: 153694 vertices, 153766 faces slice 220: 153694 vertices, 153766 faces slice 230: 153694 vertices, 153766 faces slice 240: 153694 vertices, 153766 faces slice 250: 153694 vertices, 153766 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... 153694 voxel in cpt #1: X=-72 [v=153694,e=461298,f=307532] located at (33.142902, -9.612308, 22.423145) For the whole surface: X=-72 [v=153694,e=461298,f=307532] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Jul 23 04:03:07 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Tue Jul 23 04:03:20 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Jul 23 04:03:33 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.4 mm, total surface area = 77033 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.151 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.067 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.031 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 467.196000 mris_inflate stimesec 50.648000 mris_inflate ru_maxrss 241904 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 681239 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 176 mris_inflate ru_oublock 10240 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 148902 mris_inflate ru_nivcsw 79614 #-------------------------------------------- #@# Inflation1 rh Tue Jul 23 04:04:09 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.2 mm, total surface area = 81130 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.061 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.054 (target=0.015) step 040: RMS=0.052 (target=0.015) step 045: RMS=0.050 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.049 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 484.088000 mris_inflate stimesec 91.732000 mris_inflate ru_maxrss 255252 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 771036 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10816 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 167534 mris_inflate ru_nivcsw 87360 #-------------------------------------------- #@# QSphere lh Tue Jul 23 04:04:46 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.54 (0.00-->6.50) (max @ vno 107446 --> 107447) face area 0.02 +- 0.03 (-0.03-->0.56) == Number of threads available to mris_sphere for OpenMP = 64 == scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.343, avgs=0 005/300: dt: 0.9000, rms radial error=176.084, avgs=0 010/300: dt: 0.9000, rms radial error=175.529, avgs=0 015/300: dt: 0.9000, rms radial error=174.799, avgs=0 020/300: dt: 0.9000, rms radial error=173.968, avgs=0 025/300: dt: 0.9000, rms radial error=173.078, avgs=0 030/300: dt: 0.9000, rms radial error=172.155, avgs=0 035/300: dt: 0.9000, rms radial error=171.215, avgs=0 040/300: dt: 0.9000, rms radial error=170.267, avgs=0 045/300: dt: 0.9000, rms radial error=169.318, avgs=0 050/300: dt: 0.9000, rms radial error=168.373, avgs=0 055/300: dt: 0.9000, rms radial error=167.430, avgs=0 060/300: dt: 0.9000, rms radial error=166.490, avgs=0 065/300: dt: 0.9000, rms radial error=165.555, avgs=0 070/300: dt: 0.9000, rms radial error=164.624, avgs=0 075/300: dt: 0.9000, rms radial error=163.698, avgs=0 080/300: dt: 0.9000, rms radial error=162.777, avgs=0 085/300: dt: 0.9000, rms radial error=161.862, avgs=0 090/300: dt: 0.9000, rms radial error=160.951, avgs=0 095/300: dt: 0.9000, rms radial error=160.045, avgs=0 100/300: dt: 0.9000, rms radial error=159.144, avgs=0 105/300: dt: 0.9000, rms radial error=158.248, avgs=0 110/300: dt: 0.9000, rms radial error=157.358, avgs=0 115/300: dt: 0.9000, rms radial error=156.472, avgs=0 120/300: dt: 0.9000, rms radial error=155.590, avgs=0 125/300: dt: 0.9000, rms radial error=154.714, avgs=0 130/300: dt: 0.9000, rms radial error=153.842, avgs=0 135/300: dt: 0.9000, rms radial error=152.976, avgs=0 140/300: dt: 0.9000, rms radial error=152.114, avgs=0 145/300: dt: 0.9000, rms radial error=151.257, avgs=0 150/300: dt: 0.9000, rms radial error=150.404, avgs=0 155/300: dt: 0.9000, rms radial error=149.557, avgs=0 160/300: dt: 0.9000, rms radial error=148.715, avgs=0 165/300: dt: 0.9000, rms radial error=147.878, avgs=0 170/300: dt: 0.9000, rms radial error=147.045, avgs=0 175/300: dt: 0.9000, rms radial error=146.217, avgs=0 180/300: dt: 0.9000, rms radial error=145.393, avgs=0 185/300: dt: 0.9000, rms radial error=144.574, avgs=0 190/300: dt: 0.9000, rms radial error=143.760, avgs=0 195/300: dt: 0.9000, rms radial error=142.950, avgs=0 200/300: dt: 0.9000, rms radial error=142.144, avgs=0 205/300: dt: 0.9000, rms radial error=141.343, avgs=0 210/300: dt: 0.9000, rms radial error=140.547, avgs=0 215/300: dt: 0.9000, rms radial error=139.755, avgs=0 220/300: dt: 0.9000, rms radial error=138.968, avgs=0 225/300: dt: 0.9000, rms radial error=138.185, avgs=0 230/300: dt: 0.9000, rms radial error=137.406, avgs=0 235/300: dt: 0.9000, rms radial error=136.632, avgs=0 240/300: dt: 0.9000, rms radial error=135.862, avgs=0 245/300: dt: 0.9000, rms radial error=135.096, avgs=0 250/300: dt: 0.9000, rms radial error=134.334, avgs=0 255/300: dt: 0.9000, rms radial error=133.577, avgs=0 260/300: dt: 0.9000, rms radial error=132.824, avgs=0 265/300: dt: 0.9000, rms radial error=132.075, avgs=0 270/300: dt: 0.9000, rms radial error=131.331, avgs=0 275/300: dt: 0.9000, rms radial error=130.590, avgs=0 280/300: dt: 0.9000, rms radial error=129.854, avgs=0 285/300: dt: 0.9000, rms radial error=129.121, avgs=0 290/300: dt: 0.9000, rms radial error=128.393, avgs=0 295/300: dt: 0.9000, rms radial error=127.669, avgs=0 300/300: dt: 0.9000, rms radial error=126.949, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17059.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2837.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 3 (K=160.0), pass 1, starting sse = 279.79 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/13 = 0.00999 epoch 4 (K=640.0), pass 1, starting sse = 12.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.40/22 = 0.01804 final distance error %24.26 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 2085.456000 mris_sphere stimesec 247.716000 mris_sphere ru_maxrss 242488 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 3120344 mris_sphere ru_majflt 3 mris_sphere ru_nswap 0 mris_sphere ru_inblock 368 mris_sphere ru_oublock 10240 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 645808 mris_sphere ru_nivcsw 371853 FSRUNTIME@ mris_sphere 0.0622 hours 1 threads #-------------------------------------------- #@# QSphere rh Tue Jul 23 04:08:30 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.55 (0.00-->5.91) (max @ vno 92070 --> 92090) face area 0.02 +- 0.03 (-0.12-->0.47) == Number of threads available to mris_sphere for OpenMP = 64 == scaling brain by 0.305... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.221, avgs=0 005/300: dt: 0.9000, rms radial error=175.963, avgs=0 010/300: dt: 0.9000, rms radial error=175.410, avgs=0 015/300: dt: 0.9000, rms radial error=174.685, avgs=0 020/300: dt: 0.9000, rms radial error=173.859, avgs=0 025/300: dt: 0.9000, rms radial error=172.975, avgs=0 030/300: dt: 0.9000, rms radial error=172.060, avgs=0 035/300: dt: 0.9000, rms radial error=171.127, avgs=0 040/300: dt: 0.9000, rms radial error=170.186, avgs=0 045/300: dt: 0.9000, rms radial error=169.243, avgs=0 050/300: dt: 0.9000, rms radial error=168.300, avgs=0 055/300: dt: 0.9000, rms radial error=167.360, avgs=0 060/300: dt: 0.9000, rms radial error=166.423, avgs=0 065/300: dt: 0.9000, rms radial error=165.490, avgs=0 070/300: dt: 0.9000, rms radial error=164.561, avgs=0 075/300: dt: 0.9000, rms radial error=163.637, avgs=0 080/300: dt: 0.9000, rms radial error=162.718, avgs=0 085/300: dt: 0.9000, rms radial error=161.804, avgs=0 090/300: dt: 0.9000, rms radial error=160.894, avgs=0 095/300: dt: 0.9000, rms radial error=159.989, avgs=0 100/300: dt: 0.9000, rms radial error=159.089, avgs=0 105/300: dt: 0.9000, rms radial error=158.194, avgs=0 110/300: dt: 0.9000, rms radial error=157.304, avgs=0 115/300: dt: 0.9000, rms radial error=156.418, avgs=0 120/300: dt: 0.9000, rms radial error=155.537, avgs=0 125/300: dt: 0.9000, rms radial error=154.661, avgs=0 130/300: dt: 0.9000, rms radial error=153.789, avgs=0 135/300: dt: 0.9000, rms radial error=152.923, avgs=0 140/300: dt: 0.9000, rms radial error=152.061, avgs=0 145/300: dt: 0.9000, rms radial error=151.203, avgs=0 150/300: dt: 0.9000, rms radial error=150.351, avgs=0 155/300: dt: 0.9000, rms radial error=149.502, avgs=0 160/300: dt: 0.9000, rms radial error=148.659, avgs=0 165/300: dt: 0.9000, rms radial error=147.821, avgs=0 170/300: dt: 0.9000, rms radial error=146.986, avgs=0 175/300: dt: 0.9000, rms radial error=146.157, avgs=0 180/300: dt: 0.9000, rms radial error=145.333, avgs=0 185/300: dt: 0.9000, rms radial error=144.513, avgs=0 190/300: dt: 0.9000, rms radial error=143.697, avgs=0 195/300: dt: 0.9000, rms radial error=142.886, avgs=0 200/300: dt: 0.9000, rms radial error=142.080, avgs=0 205/300: dt: 0.9000, rms radial error=141.278, avgs=0 210/300: dt: 0.9000, rms radial error=140.481, avgs=0 215/300: dt: 0.9000, rms radial error=139.688, avgs=0 220/300: dt: 0.9000, rms radial error=138.900, avgs=0 225/300: dt: 0.9000, rms radial error=138.116, avgs=0 230/300: dt: 0.9000, rms radial error=137.336, avgs=0 235/300: dt: 0.9000, rms radial error=136.561, avgs=0 240/300: dt: 0.9000, rms radial error=135.790, avgs=0 245/300: dt: 0.9000, rms radial error=135.024, avgs=0 250/300: dt: 0.9000, rms radial error=134.261, avgs=0 255/300: dt: 0.9000, rms radial error=133.504, avgs=0 260/300: dt: 0.9000, rms radial error=132.750, avgs=0 265/300: dt: 0.9000, rms radial error=132.001, avgs=0 270/300: dt: 0.9000, rms radial error=131.255, avgs=0 275/300: dt: 0.9000, rms radial error=130.514, avgs=0 280/300: dt: 0.9000, rms radial error=129.777, avgs=0 285/300: dt: 0.9000, rms radial error=129.045, avgs=0 290/300: dt: 0.9000, rms radial error=128.316, avgs=0 295/300: dt: 0.9000, rms radial error=127.592, avgs=0 300/300: dt: 0.9000, rms radial error=126.870, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18063.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 2 (K=40.0), pass 1, starting sse = 3040.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 332.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00667 epoch 4 (K=640.0), pass 1, starting sse = 28.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00728 final distance error %26.03 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 1854.556000 mris_sphere stimesec 192.240000 mris_sphere ru_maxrss 255864 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 2605757 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10816 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 617930 mris_sphere ru_nivcsw 324855 FSRUNTIME@ mris_sphere 0.0560 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Tue Jul 23 04:11:52 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Tue Jul 23 04:11:52 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Tue Jul 23 04:11:52 EDT 2019 mris_fix_topology -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 seg lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-14 (nv=145482, nf=290992, ne=436488, g=8) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 1992 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 15 defects to be corrected 0 vertices coincident reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7187 (-4.8593) -vertex loglikelihood: -6.8825 (-3.4412) -normal dot loglikelihood: -3.6129 (-3.6129) -quad curv loglikelihood: -6.4777 (-3.2388) Total Loglikelihood : -26.6917 CORRECTING DEFECT 0 (vertices=30, convex hull=61, v0=4236) After retessellation of defect 0 (v0=4236), euler #=-12 (144359,432797,288426) : difference with theory (-12) = 0 CORRECTING DEFECT 1 (vertices=6, convex hull=24, v0=71020) After retessellation of defect 1 (v0=71020), euler #=-11 (144360,432807,288436) : difference with theory (-11) = 0 CORRECTING DEFECT 2 (vertices=486, convex hull=58, v0=74706) After retessellation of defect 2 (v0=74706), euler #=-10 (144378,432888,288500) : difference with theory (-10) = 0 CORRECTING DEFECT 3 (vertices=19, convex hull=32, v0=84560) After retessellation of defect 3 (v0=84560), euler #=-9 (144382,432911,288520) : difference with theory (-9) = 0 CORRECTING DEFECT 4 (vertices=6, convex hull=24, v0=91813) After retessellation of defect 4 (v0=91813), euler #=-8 (144383,432921,288530) : difference with theory (-8) = 0 CORRECTING DEFECT 5 (vertices=24, convex hull=51, v0=93881) After retessellation of defect 5 (v0=93881), euler #=-7 (144395,432979,288577) : difference with theory (-7) = 0 CORRECTING DEFECT 6 (vertices=72, convex hull=97, v0=96427) After retessellation of defect 6 (v0=96427), euler #=-6 (144419,433092,288667) : difference with theory (-6) = 0 CORRECTING DEFECT 7 (vertices=65, convex hull=49, v0=98479) After retessellation of defect 7 (v0=98479), euler #=-5 (144440,433179,288734) : difference with theory (-5) = 0 CORRECTING DEFECT 8 (vertices=163, convex hull=43, v0=100757) After retessellation of defect 8 (v0=100757), euler #=-4 (144449,433226,288773) : difference with theory (-4) = 0 CORRECTING DEFECT 9 (vertices=6, convex hull=25, v0=105485) After retessellation of defect 9 (v0=105485), euler #=-3 (144452,433243,288788) : difference with theory (-3) = 0 CORRECTING DEFECT 10 (vertices=50, convex hull=72, v0=113384) After retessellation of defect 10 (v0=113384), euler #=-2 (144470,433328,288856) : difference with theory (-2) = 0 CORRECTING DEFECT 11 (vertices=26, convex hull=51, v0=121997) After retessellation of defect 11 (v0=121997), euler #=-1 (144484,433387,288902) : difference with theory (-1) = 0 CORRECTING DEFECT 12 (vertices=26, convex hull=47, v0=123863) After retessellation of defect 12 (v0=123863), euler #=0 (144493,433433,288940) : difference with theory (0) = 0 CORRECTING DEFECT 13 (vertices=40, convex hull=81, v0=124107) After retessellation of defect 13 (v0=124107), euler #=1 (144519,433540,289022) : difference with theory (1) = 0 CORRECTING DEFECT 14 (vertices=118, convex hull=35, v0=125919) After retessellation of defect 14 (v0=125919), euler #=2 (144528,433578,289052) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.11-->7.12) (max @ vno 96963 --> 98157) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.11-->7.12) (max @ vno 96963 --> 98157) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 50 mutations (31.1%), 111 crossovers (68.9%), 12 vertices were eliminated building final representation... 954 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=144528, nf=289052, ne=433578, g=0) writing corrected surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 10.4 minutes 0 defective edges removing intersecting faces 000: 47 intersecting mris_fix_topology utimesec 679.568000 mris_fix_topology stimesec 4.272000 mris_fix_topology ru_maxrss 460996 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 2303808 mris_fix_topology ru_majflt 2 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 272 mris_fix_topology ru_oublock 13600 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 22977 mris_fix_topology ru_nivcsw 64481 FSRUNTIME@ mris_fix_topology lh 0.1741 hours 1 threads #@# Fix Topology rh Tue Jul 23 04:22:19 EDT 2019 mris_fix_topology -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 seg rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-72 (nv=153694, nf=307532, ne=461298, g=37) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 13871 ambiguous faces found in tessellation segmenting defects... 30 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 21 into 19 29 defects to be corrected 0 vertices coincident reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7514 (-4.8757) -vertex loglikelihood: -6.9104 (-3.4552) -normal dot loglikelihood: -3.6367 (-3.6367) -quad curv loglikelihood: -6.4117 (-3.2058) Total Loglikelihood : -26.7103 CORRECTING DEFECT 0 (vertices=31, convex hull=63, v0=4992) After retessellation of defect 0 (v0=4992), euler #=-27 (146136,437216,291053) : difference with theory (-26) = 1 CORRECTING DEFECT 1 (vertices=17, convex hull=53, v0=36544) After retessellation of defect 1 (v0=36544), euler #=-26 (146143,437259,291090) : difference with theory (-25) = 1 CORRECTING DEFECT 2 (vertices=28, convex hull=51, v0=43606) After retessellation of defect 2 (v0=43606), euler #=-25 (146160,437329,291144) : difference with theory (-24) = 1 CORRECTING DEFECT 3 (vertices=2754, convex hull=434, v0=51260) XL defect detected... normal vector of length zero at vertex 148008 with 3 faces normal vector of length zero at vertex 147732 with 4 faces normal vector of length zero at vertex 147732 with 4 faces normal vector of length zero at vertex 147732 with 4 faces normal vector of length zero at vertex 147732 with 4 faces After retessellation of defect 3 (v0=51260), euler #=-24 (146208,437694,291462) : difference with theory (-23) = 1 CORRECTING DEFECT 4 (vertices=8, convex hull=19, v0=53480) After retessellation of defect 4 (v0=53480), euler #=-23 (146209,437701,291469) : difference with theory (-22) = 1 CORRECTING DEFECT 5 (vertices=562, convex hull=191, v0=62397) After retessellation of defect 5 (v0=62397), euler #=-22 (146310,438093,291761) : difference with theory (-21) = 1 CORRECTING DEFECT 6 (vertices=37, convex hull=59, v0=70766) After retessellation of defect 6 (v0=70766), euler #=-21 (146322,438147,291804) : difference with theory (-20) = 1 CORRECTING DEFECT 7 (vertices=882, convex hull=469, v0=76091) L defect detected... After retessellation of defect 7 (v0=76091), euler #=-20 (146450,438763,292293) : difference with theory (-19) = 1 CORRECTING DEFECT 8 (vertices=284, convex hull=81, v0=76471) After retessellation of defect 8 (v0=76471), euler #=-19 (146478,438878,292381) : difference with theory (-18) = 1 CORRECTING DEFECT 9 (vertices=217, convex hull=55, v0=78114) After retessellation of defect 9 (v0=78114), euler #=-18 (146503,438976,292455) : difference with theory (-17) = 1 CORRECTING DEFECT 10 (vertices=8, convex hull=18, v0=80529) After retessellation of defect 10 (v0=80529), euler #=-17 (146504,438985,292464) : difference with theory (-16) = 1 CORRECTING DEFECT 11 (vertices=1792, convex hull=278, v0=84100) After retessellation of defect 11 (v0=84100), euler #=-16 (146593,439390,292781) : difference with theory (-15) = 1 CORRECTING DEFECT 12 (vertices=15, convex hull=32, v0=84465) After retessellation of defect 12 (v0=84465), euler #=-15 (146594,439403,292794) : difference with theory (-14) = 1 CORRECTING DEFECT 13 (vertices=6, convex hull=19, v0=86485) After retessellation of defect 13 (v0=86485), euler #=-14 (146596,439415,292805) : difference with theory (-13) = 1 CORRECTING DEFECT 14 (vertices=83, convex hull=68, v0=86697) After retessellation of defect 14 (v0=86697), euler #=-13 (146618,439508,292877) : difference with theory (-12) = 1 CORRECTING DEFECT 15 (vertices=189, convex hull=74, v0=88289) After retessellation of defect 15 (v0=88289), euler #=-12 (146629,439574,292933) : difference with theory (-11) = 1 CORRECTING DEFECT 16 (vertices=68, convex hull=87, v0=88367) After retessellation of defect 16 (v0=88367), euler #=-11 (146647,439667,293009) : difference with theory (-10) = 1 CORRECTING DEFECT 17 (vertices=31, convex hull=58, v0=91030) After retessellation of defect 17 (v0=91030), euler #=-10 (146666,439749,293073) : difference with theory (-9) = 1 CORRECTING DEFECT 18 (vertices=13, convex hull=28, v0=92783) After retessellation of defect 18 (v0=92783), euler #=-9 (146668,439762,293085) : difference with theory (-8) = 1 CORRECTING DEFECT 19 (vertices=135, convex hull=193, v0=99435) After retessellation of defect 19 (v0=99435), euler #=-7 (146689,439907,293211) : difference with theory (-7) = 0 CORRECTING DEFECT 20 (vertices=34, convex hull=56, v0=100345) After retessellation of defect 20 (v0=100345), euler #=-6 (146706,439979,293267) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=89, convex hull=41, v0=103494) After retessellation of defect 21 (v0=103494), euler #=-5 (146716,440023,293302) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=26, convex hull=30, v0=104900) After retessellation of defect 22 (v0=104900), euler #=-4 (146722,440049,293323) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=123, convex hull=46, v0=111063) After retessellation of defect 23 (v0=111063), euler #=-3 (146731,440095,293361) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=28, convex hull=55, v0=118678) After retessellation of defect 24 (v0=118678), euler #=-2 (146748,440166,293416) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=13, convex hull=30, v0=149435) After retessellation of defect 25 (v0=149435), euler #=-1 (146749,440179,293429) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=35, convex hull=66, v0=150272) After retessellation of defect 26 (v0=150272), euler #=0 (146758,440230,293472) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=39, convex hull=54, v0=151374) After retessellation of defect 27 (v0=151374), euler #=1 (146763,440269,293507) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=19, convex hull=33, v0=152635) After retessellation of defect 28 (v0=152635), euler #=2 (146765,440289,293526) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.06-->10.29) (max @ vno 81845 --> 89815) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.06-->10.29) (max @ vno 81845 --> 89815) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 127 mutations (34.7%), 239 crossovers (65.3%), 834 vertices were eliminated building final representation... 6929 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146765, nf=293526, ne=440289, g=0) writing corrected surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 47.8 minutes 0 defective edges removing intersecting faces 000: 432 intersecting 001: 17 intersecting mris_fix_topology utimesec 2926.500000 mris_fix_topology stimesec 6.440000 mris_fix_topology ru_maxrss 507192 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 3964759 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13952 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 23347 mris_fix_topology ru_nivcsw 252032 FSRUNTIME@ mris_fix_topology rh 0.7967 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 144528 - 433578 + 289052 = 2 --> 0 holes F =2V-4: 289052 = 289056-4 (0) 2E=3F: 867156 = 867156 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 146765 - 440289 + 293526 = 2 --> 0 holes F =2V-4: 293526 = 293530-4 (0) 2E=3F: 880578 = 880578 (0) total defect index = 0 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 11 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 94 intersecting 001: 11 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Jul 23 05:10:25 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs seg lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/filled.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/brain.finalsurfs.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/../mri/aseg.presurf.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... 28879 bright wm thresholded. 1175 bright non-wm voxels segmented. reading original surface position from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.orig... computing class statistics... border white: 276765 voxels (1.65%) border gray 337536 voxels (2.01%) WM (99.0): 97.6 +- 10.4 [70.0 --> 110.0] GM (58.0) : 59.2 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 37.8 (was 70) setting MAX_BORDER_WHITE to 115.4 (was 105) setting MIN_BORDER_WHITE to 50.0 (was 85) setting MAX_CSF to 25.6 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 37.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 13.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.41) (max @ vno 98156 --> 98157) face area 0.28 +- 0.12 (0.00-->1.81) mean absolute distance = 0.57 +- 0.63 4463 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-7.0, GM=50+-10.4 mean inside = 91.5, mean outside = 63.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=69.0, 55 (55) missing vertices, mean dist 0.3 [0.4 (%32.0)->0.7 (%68.0))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.24 (0.10-->3.37) (max @ vno 98156 --> 98157) face area 0.28 +- 0.12 (0.00-->1.46) mean absolute distance = 0.25 +- 0.40 2921 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6489334.0, rms=14.627 001: dt: 0.5000, sse=3516780.2, rms=10.338 (29.325%) 002: dt: 0.5000, sse=2333374.8, rms=8.013 (22.487%) 003: dt: 0.5000, sse=1726951.2, rms=6.500 (18.879%) 004: dt: 0.5000, sse=1487901.2, rms=5.796 (10.833%) 005: dt: 0.5000, sse=1354835.9, rms=5.358 (7.557%) 006: dt: 0.5000, sse=1330668.8, rms=5.271 (1.631%) 007: dt: 0.5000, sse=1292832.9, rms=5.123 (2.806%) rms = 5.15, time step reduction 1 of 3 to 0.250... 008: dt: 0.2500, sse=912995.8, rms=3.494 (31.786%) 009: dt: 0.2500, sse=816102.4, rms=2.939 (15.894%) 010: dt: 0.2500, sse=800815.9, rms=2.833 (3.605%) rms = 2.84, time step reduction 2 of 3 to 0.125... 011: dt: 0.1250, sse=754911.5, rms=2.518 (11.112%) 012: dt: 0.1250, sse=694836.5, rms=2.024 (19.631%) 013: dt: 0.1250, sse=684966.0, rms=1.932 (4.530%) rms = 1.91, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=683031.8, rms=1.912 (1.027%) positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=73.3, 69 (25) missing vertices, mean dist -0.2 [0.3 (%77.5)->0.2 (%22.5))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= roxy, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.09-->3.27) (max @ vno 89873 --> 91057) face area 0.35 +- 0.15 (0.00-->2.19) mean absolute distance = 0.18 +- 0.29 2715 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1730374.2, rms=6.024 015: dt: 0.5000, sse=1315389.6, rms=4.616 (23.371%) rms = 5.23, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=985559.2, rms=3.052 (33.884%) 017: dt: 0.2500, sse=913564.4, rms=2.587 (15.230%) 018: dt: 0.2500, sse=873099.1, rms=2.289 (11.539%) rms = 2.35, time step reduction 2 of 3 to 0.125... 019: dt: 0.1250, sse=844988.6, rms=2.050 (10.421%) 020: dt: 0.1250, sse=811551.6, rms=1.689 (17.631%) 021: dt: 0.1250, sse=802240.3, rms=1.614 (4.396%) rms = 1.59, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=799687.6, rms=1.592 (1.387%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=75.9, 69 (19) missing vertices, mean dist -0.1 [0.2 (%71.2)->0.2 (%28.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= roxy, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.15-->3.41) (max @ vno 91067 --> 91057) face area 0.34 +- 0.15 (0.00-->2.29) mean absolute distance = 0.15 +- 0.25 2903 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1110111.0, rms=3.789 rms = 4.71, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=893067.7, rms=2.542 (32.901%) 024: dt: 0.2500, sse=813809.1, rms=1.801 (29.142%) 025: dt: 0.2500, sse=794570.4, rms=1.704 (5.413%) rms = 1.66, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=795028.2, rms=1.661 (2.547%) 027: dt: 0.1250, sse=765827.6, rms=1.358 (18.212%) rms = 1.31, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=761677.9, rms=1.309 (3.627%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=76.7, 62 (13) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.1 (%44.4))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= roxy, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=791191.3, rms=1.743 rms = 3.04, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=741936.8, rms=1.119 (35.802%) 030: dt: 0.2500, sse=736362.4, rms=0.973 (13.075%) rms = 0.96, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=730642.7, rms=0.960 (1.275%) rms = 0.93, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=734465.2, rms=0.925 (3.618%) positioning took 0.7 minutes generating cortex label... 6 non-cortical segments detected only using segment with 8057 vertices erasing segment 1 (vno[0] = 84592) erasing segment 2 (vno[0] = 90134) erasing segment 3 (vno[0] = 101159) erasing segment 4 (vno[0] = 105675) erasing segment 5 (vno[0] = 110294) writing cortex label to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.cortex.label... writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.curv writing smoothed area to lh.area writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.area vertex spacing 0.90 +- 0.24 (0.03-->3.47) (max @ vno 85359 --> 86463) face area 0.34 +- 0.15 (0.00-->2.26) refinement took 8.8 minutes #-------------------------------------------- #@# Make White Surf rh Tue Jul 23 05:19:15 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs seg rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/filled.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/brain.finalsurfs.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/../mri/aseg.presurf.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... 28879 bright wm thresholded. 1175 bright non-wm voxels segmented. reading original surface position from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.orig... computing class statistics... border white: 276765 voxels (1.65%) border gray 337536 voxels (2.01%) WM (99.0): 97.6 +- 10.4 [70.0 --> 110.0] GM (58.0) : 59.2 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 38.8 (was 70) setting MAX_BORDER_WHITE to 114.4 (was 105) setting MIN_BORDER_WHITE to 51.0 (was 85) setting MAX_CSF to 26.6 (was 40) setting MAX_GRAY to 93.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 38.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 14.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.95) (max @ vno 63968 --> 65291) face area 0.28 +- 0.12 (0.00-->4.37) mean absolute distance = 0.58 +- 0.68 4537 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-5.2, GM=51+-9.6 mean inside = 91.6, mean outside = 63.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=69.8, 76 (76) missing vertices, mean dist 0.3 [0.4 (%33.2)->0.7 (%66.8))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->4.60) (max @ vno 63968 --> 65291) face area 0.28 +- 0.13 (0.00-->3.48) mean absolute distance = 0.27 +- 0.47 2863 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6553627.0, rms=14.564 001: dt: 0.5000, sse=3476705.5, rms=10.153 (30.288%) 002: dt: 0.5000, sse=2286369.0, rms=7.806 (23.118%) 003: dt: 0.5000, sse=1705438.5, rms=6.339 (18.797%) 004: dt: 0.5000, sse=1494091.9, rms=5.721 (9.751%) 005: dt: 0.5000, sse=1374240.0, rms=5.313 (7.121%) 006: dt: 0.5000, sse=1355561.5, rms=5.259 (1.015%) 007: dt: 0.5000, sse=1313561.2, rms=5.102 (2.982%) rms = 5.15, time step reduction 1 of 3 to 0.250... 008: dt: 0.2500, sse=928144.1, rms=3.470 (31.986%) 009: dt: 0.2500, sse=830609.3, rms=2.910 (16.142%) 010: dt: 0.2500, sse=818998.6, rms=2.834 (2.632%) rms = 2.86, time step reduction 2 of 3 to 0.125... 011: dt: 0.1250, sse=771187.6, rms=2.508 (11.480%) 012: dt: 0.1250, sse=709547.8, rms=1.999 (20.300%) 013: dt: 0.1250, sse=699346.9, rms=1.907 (4.585%) rms = 1.89, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=697033.1, rms=1.886 (1.145%) positioning took 2.7 minutes inhibiting deformation at non-cortical midline structures... mean border=74.2, 96 (24) missing vertices, mean dist -0.2 [0.3 (%78.0)->0.2 (%22.0))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= roxy, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.08-->4.56) (max @ vno 63968 --> 65291) face area 0.35 +- 0.16 (0.00-->4.35) mean absolute distance = 0.19 +- 0.34 2828 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1796844.1, rms=6.123 015: dt: 0.5000, sse=1365433.6, rms=4.700 (23.237%) rms = 5.21, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=1027832.4, rms=3.159 (32.798%) 017: dt: 0.2500, sse=941477.2, rms=2.643 (16.324%) 018: dt: 0.2500, sse=897593.6, rms=2.333 (11.731%) rms = 2.39, time step reduction 2 of 3 to 0.125... 019: dt: 0.1250, sse=867753.4, rms=2.087 (10.551%) 020: dt: 0.1250, sse=830628.6, rms=1.710 (18.066%) 021: dt: 0.1250, sse=819522.5, rms=1.628 (4.808%) rms = 1.60, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=818147.1, rms=1.604 (1.485%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=76.8, 95 (9) missing vertices, mean dist -0.1 [0.2 (%71.1)->0.2 (%28.9))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= roxy, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.07-->4.57) (max @ vno 63968 --> 65291) face area 0.34 +- 0.15 (0.00-->4.09) mean absolute distance = 0.16 +- 0.28 2707 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1137880.5, rms=3.821 rms = 4.72, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=917805.8, rms=2.596 (32.058%) 024: dt: 0.2500, sse=828781.2, rms=1.841 (29.069%) 025: dt: 0.2500, sse=820763.1, rms=1.751 (4.897%) rms = 1.72, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=813144.3, rms=1.721 (1.694%) 027: dt: 0.1250, sse=786251.6, rms=1.413 (17.922%) 028: dt: 0.1250, sse=780795.5, rms=1.360 (3.760%) rms = 1.36, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=781002.2, rms=1.363 (-0.250%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=77.5, 108 (6) missing vertices, mean dist -0.0 [0.2 (%55.2)->0.2 (%44.8))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= roxy, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=813959.4, rms=1.809 rms = 3.09, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=762408.6, rms=1.207 (33.260%) 031: dt: 0.2500, sse=753494.9, rms=1.064 (11.865%) rms = 1.06, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=760584.9, rms=1.062 (0.141%) 033: dt: 0.1250, sse=747384.4, rms=1.009 (5.015%) rms = 0.99, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=746257.1, rms=0.993 (1.584%) positioning took 0.9 minutes generating cortex label... 5 non-cortical segments detected only using segment with 8161 vertices erasing segment 1 (vno[0] = 85654) erasing segment 2 (vno[0] = 100150) erasing segment 3 (vno[0] = 103494) erasing segment 4 (vno[0] = 107492) writing cortex label to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.cortex.label... writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.curv writing smoothed area to rh.area writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.area vertex spacing 0.90 +- 0.24 (0.04-->4.59) (max @ vno 63968 --> 65291) face area 0.34 +- 0.15 (0.00-->4.04) refinement took 9.8 minutes #-------------------------------------------- #@# Smooth2 lh Tue Jul 23 05:29:02 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Tue Jul 23 05:29:14 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Jul 23 05:29:26 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_inflate -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.5 mm, total surface area = 88983 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 466.452000 mris_inflate stimesec 69.032000 mris_inflate ru_maxrss 240556 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 663425 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11304 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 147995 mris_inflate ru_nivcsw 83556 #-------------------------------------------- #@# Inflation2 rh Tue Jul 23 05:30:02 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_inflate -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.6 mm, total surface area = 90415 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 459.964000 mris_inflate stimesec 96.744000 mris_inflate ru_maxrss 244376 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 725602 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11480 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 152059 mris_inflate ru_nivcsw 83800 #-------------------------------------------- #@# Curv .H and .K lh Tue Jul 23 05:30:38 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf mris_curvature -w lh.white.preaparc total integrated curvature = 10.546*4pi (132.524) --> -10 handles ICI = 158.3, FI = 1933.7, variation=29337.282 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. 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 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 163 vertices thresholded to be in k1 ~ [-0.16 0.49], k2 ~ [-0.10 0.06] total integrated curvature = 0.548*4pi (6.891) --> 0 handles ICI = 1.5, FI = 9.6, variation=162.963 121 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 148 vertices thresholded to be in [-0.11 0.21] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh Tue Jul 23 05:32:44 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf mris_curvature -w rh.white.preaparc total integrated curvature = 14.951*4pi (187.875) --> -14 handles ICI = 163.3, FI = 1969.6, variation=29893.659 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. 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 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 191 vertices thresholded to be in k1 ~ [-0.87 0.35], k2 ~ [-0.10 0.19] total integrated curvature = 0.484*4pi (6.078) --> 1 handles ICI = 1.4, FI = 9.8, variation=164.820 126 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 114 vertices thresholded to be in [-0.19 0.17] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Tue Jul 23 05:34:52 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm seg lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ seg/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 247 ] Gb_filter = 0 WARN: S lookup min: -0.594826 WARN: S explicit min: 0.000000 vertex = 342 #----------------------------------------- #@# Curvature Stats rh Tue Jul 23 05:35:01 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm seg rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ seg/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 267 ] Gb_filter = 0 WARN: S lookup min: -0.208043 WARN: S explicit min: 0.000000 vertex = 338 #-------------------------------------------- #@# Sphere lh Tue Jul 23 05:35:09 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_sphere -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 64 == scaling brain by 0.284... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= roxy, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %41.48 pass 1: epoch 2 of 3 starting distance error %19.69 unfolding complete - removing small folds... starting distance error %19.59 removing remaining folds... final distance error %19.61 MRISunfold() return, current seed 1234 -01: dt=0.0000, 58 negative triangles 125: dt=0.9900, 58 negative triangles 126: dt=0.9900, 34 negative triangles 127: dt=0.9900, 22 negative triangles 128: dt=0.9900, 22 negative triangles 129: dt=0.9900, 16 negative triangles 130: dt=0.9900, 14 negative triangles 131: dt=0.9900, 14 negative triangles 132: dt=0.9900, 6 negative triangles 133: dt=0.9900, 9 negative triangles 134: dt=0.9900, 9 negative triangles 135: dt=0.9900, 4 negative triangles 136: dt=0.9900, 5 negative triangles 137: dt=0.9900, 4 negative triangles 138: dt=0.9900, 2 negative triangles 139: dt=0.9900, 1 negative triangles 140: dt=0.9900, 2 negative triangles 141: dt=0.9900, 1 negative triangles 142: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.24 hours mris_sphere utimesec 16293.412000 mris_sphere stimesec 1352.076000 mris_sphere ru_maxrss 326712 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 22876213 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10168 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 4141195 mris_sphere ru_nivcsw 2631738 FSRUNTIME@ mris_sphere 0.2360 hours 1 threads #-------------------------------------------- #@# Sphere rh Tue Jul 23 05:49:19 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_sphere -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 64 == scaling brain by 0.285... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= roxy, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.86 pass 1: epoch 2 of 3 starting distance error %19.75 unfolding complete - removing small folds... starting distance error %19.69 removing remaining folds... final distance error %19.70 MRISunfold() return, current seed 1234 -01: dt=0.0000, 118 negative triangles 179: dt=0.9900, 118 negative triangles 180: dt=0.9900, 49 negative triangles 181: dt=0.9900, 43 negative triangles 182: dt=0.9900, 36 negative triangles 183: dt=0.9900, 34 negative triangles 184: dt=0.9900, 28 negative triangles 185: dt=0.9900, 37 negative triangles 186: dt=0.9900, 29 negative triangles 187: dt=0.9900, 32 negative triangles 188: dt=0.9900, 32 negative triangles 189: dt=0.9900, 32 negative triangles 190: dt=0.9900, 22 negative triangles 191: dt=0.9900, 14 negative triangles 192: dt=0.9900, 11 negative triangles 193: dt=0.9900, 12 negative triangles 194: dt=0.9900, 8 negative triangles 195: dt=0.9900, 5 negative triangles 196: dt=0.9900, 3 negative triangles 197: dt=0.9900, 4 negative triangles 198: dt=0.9900, 2 negative triangles 199: dt=0.9900, 1 negative triangles 200: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.43 hours mris_sphere utimesec 34028.100000 mris_sphere stimesec 2156.464000 mris_sphere ru_maxrss 331532 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 40345563 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10328 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8349899 mris_sphere ru_nivcsw 5241240 FSRUNTIME@ mris_sphere 0.4296 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue Jul 23 06:15:05 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_register -curv -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts cmdline mris_register -curv -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= roxy, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= roxy, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.460 curvature mean = 0.026, std = 0.818 curvature mean = 0.015, std = 0.853 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 374605.4, tmin=1.4131 d=32.00 min @ (0.00, -8.00, -8.00) sse = 302598.9, tmin=2.8366 d=16.00 min @ (4.00, 4.00, 0.00) sse = 281615.9, tmin=4.2855 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 279752.1, tmin=5.7439 d=4.00 min @ (0.00, 0.00, 1.00) sse = 279020.4, tmin=7.2180 d=2.00 min @ (0.50, 0.50, -0.50) sse = 278490.5, tmin=8.6957 d=1.00 min @ (0.25, 0.00, 0.25) sse = 278417.1, tmin=10.1811 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 278391.4, tmin=11.6587 tol=1.0e+00, sigma=0.5, host= roxy, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 11.66 min curvature mean = -0.003, std = 0.820 curvature mean = 0.005, std = 0.939 curvature mean = -0.008, std = 0.830 curvature mean = 0.002, std = 0.975 curvature mean = -0.011, std = 0.830 curvature mean = 0.000, std = 0.990 2 Reading smoothwm curvature mean = -0.023, std = 0.281 curvature mean = 0.039, std = 0.246 curvature mean = 0.056, std = 0.341 curvature mean = 0.037, std = 0.303 curvature mean = 0.034, std = 0.537 curvature mean = 0.037, std = 0.329 curvature mean = 0.019, std = 0.684 curvature mean = 0.037, std = 0.340 curvature mean = 0.007, std = 0.795 MRISregister() return, current seed 0 -01: dt=0.0000, 18 negative triangles 116: dt=0.9900, 18 negative triangles expanding nbhd size to 1 117: dt=0.9900, 30 negative triangles 118: dt=0.9900, 16 negative triangles 119: dt=0.9900, 16 negative triangles 120: dt=0.9900, 15 negative triangles 121: dt=0.9900, 16 negative triangles 122: dt=0.9900, 12 negative triangles 123: dt=0.9900, 8 negative triangles 124: dt=0.9900, 8 negative triangles 125: dt=0.9900, 6 negative triangles 126: dt=0.9900, 5 negative triangles 127: dt=0.9900, 4 negative triangles 128: dt=0.9900, 5 negative triangles 129: dt=0.9900, 6 negative triangles 130: dt=0.9900, 4 negative triangles 131: dt=0.9900, 3 negative triangles 132: dt=0.9900, 3 negative triangles 133: dt=0.9900, 4 negative triangles 134: dt=0.9900, 4 negative triangles 135: dt=0.9900, 2 negative triangles 136: dt=0.9900, 2 negative triangles 137: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.09 hours mris_register utimesec 80745.700000 mris_register stimesec 2645.444000 mris_register ru_maxrss 293260 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 43069806 mris_register ru_majflt 1 mris_register ru_nswap 0 mris_register ru_inblock 128 mris_register ru_oublock 10176 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 21063780 mris_register ru_nivcsw 11885847 FSRUNTIME@ mris_register 1.0933 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Tue Jul 23 07:20:41 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_register -curv -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts cmdline mris_register -curv -rusage /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= roxy, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= roxy, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 5.604 curvature mean = 0.026, std = 0.803 curvature mean = 0.016, std = 0.853 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 331413.9, tmin=1.4004 d=32.00 min @ (-8.00, 0.00, 0.00) sse = 296082.3, tmin=2.8407 d=16.00 min @ (0.00, -4.00, 0.00) sse = 258765.7, tmin=4.2821 d=8.00 min @ (0.00, 0.00, -2.00) sse = 249357.6, tmin=5.7350 d=2.00 min @ (0.50, 0.50, 0.00) sse = 248661.0, tmin=8.6657 d=0.50 min @ (-0.12, -0.12, -0.12) sse = 248588.1, tmin=11.6026 tol=1.0e+00, sigma=0.5, host= roxy, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 11.60 min curvature mean = -0.009, std = 0.802 curvature mean = 0.007, std = 0.941 curvature mean = -0.015, std = 0.807 curvature mean = 0.003, std = 0.976 curvature mean = -0.017, std = 0.807 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.023, std = 0.281 curvature mean = 0.034, std = 0.238 curvature mean = 0.062, std = 0.339 curvature mean = 0.030, std = 0.296 curvature mean = 0.036, std = 0.531 curvature mean = 0.029, std = 0.323 curvature mean = 0.021, std = 0.676 curvature mean = 0.029, std = 0.334 curvature mean = 0.007, std = 0.789 MRISregister() return, current seed 0 -01: dt=0.0000, 45 negative triangles 117: dt=0.9900, 45 negative triangles expanding nbhd size to 1 118: dt=0.9900, 54 negative triangles 119: dt=0.9900, 44 negative triangles 120: dt=0.9900, 43 negative triangles 121: dt=0.9900, 43 negative triangles 122: dt=0.9900, 43 negative triangles 123: dt=0.9900, 36 negative triangles 124: dt=0.9900, 32 negative triangles 125: dt=0.9900, 32 negative triangles 126: dt=0.9900, 29 negative triangles 127: dt=0.9900, 26 negative triangles 128: dt=0.9900, 26 negative triangles 129: dt=0.9900, 27 negative triangles 130: dt=0.9900, 25 negative triangles 131: dt=0.9900, 26 negative triangles 132: dt=0.9900, 25 negative triangles 133: dt=0.9900, 26 negative triangles 134: dt=0.9900, 23 negative triangles 135: dt=0.9900, 23 negative triangles 136: dt=0.9900, 21 negative triangles 137: dt=0.9900, 20 negative triangles 138: dt=0.9900, 19 negative triangles 139: dt=0.9900, 15 negative triangles 140: dt=0.9900, 15 negative triangles 141: dt=0.9900, 15 negative triangles 142: dt=0.9900, 12 negative triangles 143: dt=0.9900, 12 negative triangles 144: dt=0.9900, 13 negative triangles 145: dt=0.9900, 11 negative triangles 146: dt=0.9900, 7 negative triangles 147: dt=0.9900, 6 negative triangles 148: dt=0.9900, 6 negative triangles 149: dt=0.9900, 6 negative triangles 150: dt=0.9900, 6 negative triangles 151: dt=0.9900, 6 negative triangles 152: dt=0.9900, 3 negative triangles 153: dt=0.9900, 4 negative triangles 154: dt=0.9900, 3 negative triangles 155: dt=0.9900, 5 negative triangles 156: dt=0.9900, 4 negative triangles 157: dt=0.9900, 3 negative triangles 158: dt=0.9900, 2 negative triangles 159: dt=0.9900, 2 negative triangles 160: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.12 hours mris_register utimesec 80269.708000 mris_register stimesec 2292.652000 mris_register ru_maxrss 298196 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 43091851 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10328 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 21208292 mris_register ru_nivcsw 11684334 FSRUNTIME@ mris_register 1.1240 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue Jul 23 08:28:08 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Tue Jul 23 08:28:11 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Jul 23 08:28:15 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Tue Jul 23 08:28:19 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Jul 23 08:28:22 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 seg lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1414 labels changed using aseg relabeling using gibbs priors... 000: 3215 changed, 144528 examined... 001: 722 changed, 13582 examined... 002: 174 changed, 4028 examined... 003: 57 changed, 1030 examined... 004: 23 changed, 337 examined... 005: 9 changed, 143 examined... 006: 5 changed, 43 examined... 007: 1 changed, 26 examined... 008: 1 changed, 7 examined... 009: 1 changed, 7 examined... 010: 0 changed, 5 examined... 208 labels changed using aseg 000: 125 total segments, 74 labels (459 vertices) changed 001: 49 total segments, 10 labels (21 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1619 vertices marked for relabeling... 1619 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 38 seconds. #----------------------------------------- #@# Cortical Parc rh Tue Jul 23 08:29:01 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 seg rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1655 labels changed using aseg relabeling using gibbs priors... 000: 2990 changed, 146765 examined... 001: 697 changed, 12791 examined... 002: 175 changed, 4033 examined... 003: 56 changed, 1049 examined... 004: 27 changed, 348 examined... 005: 15 changed, 164 examined... 006: 4 changed, 79 examined... 007: 2 changed, 22 examined... 008: 1 changed, 10 examined... 009: 0 changed, 6 examined... 176 labels changed using aseg 000: 107 total segments, 68 labels (323 vertices) changed 001: 41 total segments, 2 labels (5 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1386 vertices marked for relabeling... 1386 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 30 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Jul 23 08:29:31 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs seg lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/filled.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/brain.finalsurfs.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/../mri/aseg.presurf.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... 28879 bright wm thresholded. 1175 bright non-wm voxels segmented. reading original surface position from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.orig... computing class statistics... border white: 276765 voxels (1.65%) border gray 337536 voxels (2.01%) WM (99.0): 97.6 +- 10.4 [70.0 --> 110.0] GM (58.0) : 59.2 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 37.8 (was 70) setting MAX_BORDER_WHITE to 115.4 (was 105) setting MIN_BORDER_WHITE to 50.0 (was 85) setting MAX_CSF to 25.6 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 37.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 13.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-7.0, GM=50+-10.4 mean inside = 91.5, mean outside = 63.4 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.24 (0.03-->3.47) (max @ vno 85359 --> 86463) face area 0.34 +- 0.15 (0.00-->2.25) mean absolute distance = 0.44 +- 0.59 3853 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 162 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown mean border=68.2, 64 (64) missing vertices, mean dist 0.3 [0.4 (%11.8)->0.4 (%88.2))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.10-->3.66) (max @ vno 108445 --> 107493) face area 0.34 +- 0.15 (0.00-->2.03) mean absolute distance = 0.27 +- 0.42 2833 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3718956.2, rms=10.446 001: dt: 0.5000, sse=1787880.4, rms=6.275 (39.934%) 002: dt: 0.5000, sse=1446604.4, rms=5.219 (16.828%) 003: dt: 0.5000, sse=1408210.8, rms=5.078 (2.707%) 004: dt: 0.5000, sse=1351896.2, rms=4.873 (4.020%) rms = 4.97, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=986556.7, rms=3.215 (34.033%) 006: dt: 0.2500, sse=899248.4, rms=2.663 (17.167%) 007: dt: 0.2500, sse=858180.7, rms=2.366 (11.157%) rms = 2.38, time step reduction 2 of 3 to 0.125... 008: dt: 0.1250, sse=834727.4, rms=2.173 (8.154%) 009: dt: 0.1250, sse=803839.9, rms=1.884 (13.313%) 010: dt: 0.1250, sse=797894.7, rms=1.827 (3.024%) rms = 1.82, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=797154.6, rms=1.815 (0.636%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 88 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown mean border=73.0, 74 (20) missing vertices, mean dist -0.2 [0.3 (%80.2)->0.2 (%19.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= roxy, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.09-->3.76) (max @ vno 101318 --> 100173) face area 0.36 +- 0.16 (0.00-->2.42) mean absolute distance = 0.18 +- 0.29 2523 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1835411.9, rms=6.266 012: dt: 0.5000, sse=1325471.6, rms=4.550 (27.387%) rms = 5.14, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=1003631.1, rms=3.017 (33.698%) 014: dt: 0.2500, sse=923138.8, rms=2.496 (17.269%) 015: dt: 0.2500, sse=883835.7, rms=2.179 (12.704%) rms = 2.21, time step reduction 2 of 3 to 0.125... 016: dt: 0.1250, sse=855754.0, rms=1.937 (11.105%) 017: dt: 0.1250, sse=818810.7, rms=1.555 (19.733%) 018: dt: 0.1250, sse=811743.9, rms=1.471 (5.399%) rms = 1.45, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=810449.4, rms=1.448 (1.554%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 33 points - only 0.00% unknown deleting segment 3 with 31 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 13 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown mean border=75.7, 77 (15) missing vertices, mean dist -0.1 [0.2 (%72.5)->0.2 (%27.5))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= roxy, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.08-->3.81) (max @ vno 107532 --> 106557) face area 0.35 +- 0.16 (0.00-->2.48) mean absolute distance = 0.15 +- 0.25 2167 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1128524.1, rms=3.823 rms = 4.67, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=902031.9, rms=2.529 (33.848%) 021: dt: 0.2500, sse=808875.3, rms=1.712 (32.315%) 022: dt: 0.2500, sse=802502.3, rms=1.617 (5.530%) rms = 1.59, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=795457.8, rms=1.591 (1.629%) 024: dt: 0.1250, sse=770208.0, rms=1.273 (19.990%) rms = 1.22, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=766772.1, rms=1.225 (3.762%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 35 points - only 0.00% unknown deleting segment 3 with 36 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 13 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown mean border=76.5, 64 (12) missing vertices, mean dist -0.0 [0.2 (%55.9)->0.1 (%44.1))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= roxy, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=797562.0, rms=1.717 rms = 3.03, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=747453.7, rms=1.068 (37.760%) 027: dt: 0.2500, sse=740765.3, rms=0.933 (12.641%) rms = 0.93, time step reduction 2 of 3 to 0.125... rms = 0.91, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=738530.1, rms=0.912 (2.251%) positioning took 0.8 minutes generating cortex label... 5 non-cortical segments detected only using segment with 8073 vertices erasing segment 1 (vno[0] = 84592) erasing segment 2 (vno[0] = 101159) erasing segment 3 (vno[0] = 101281) erasing segment 4 (vno[0] = 110294) writing cortex label to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.cortex.label... writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.curv writing smoothed area to lh.area writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->3.83) (max @ vno 106557 --> 107532) face area 0.34 +- 0.16 (0.00-->2.52) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=35.8, 70 (70) missing vertices, mean dist 1.6 [0.0 (%0.0)->2.7 (%100.0))] % 4 local maxima, %52 large gradients and %40 min vals, 568 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=48331088.0, rms=41.539 001: dt: 0.0500, sse=41948800.0, rms=38.656 (6.941%) 002: dt: 0.0500, sse=37366224.0, rms=36.445 (5.719%) 003: dt: 0.0500, sse=33877032.0, rms=34.667 (4.878%) 004: dt: 0.0500, sse=31084830.0, rms=33.176 (4.302%) 005: dt: 0.0500, sse=28767618.0, rms=31.885 (3.890%) 006: dt: 0.0500, sse=26791272.0, rms=30.741 (3.587%) 007: dt: 0.0500, sse=25072488.0, rms=29.711 (3.352%) 008: dt: 0.0500, sse=23556134.0, rms=28.771 (3.163%) 009: dt: 0.0500, sse=22202546.0, rms=27.905 (3.009%) 010: dt: 0.0500, sse=20982836.0, rms=27.101 (2.881%) positioning took 1.8 minutes mean border=35.6, 49 (28) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.2 (%100.0))] % 4 local maxima, %52 large gradients and %40 min vals, 531 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=22057470.0, rms=27.811 011: dt: 0.0500, sse=20947418.0, rms=27.079 (2.635%) 012: dt: 0.0500, sse=19935750.0, rms=26.393 (2.533%) 013: dt: 0.0500, sse=19010542.0, rms=25.750 (2.437%) 014: dt: 0.0500, sse=18162888.0, rms=25.146 (2.345%) 015: dt: 0.0500, sse=17383542.0, rms=24.577 (2.260%) 016: dt: 0.0500, sse=16666338.0, rms=24.042 (2.177%) 017: dt: 0.0500, sse=16006172.0, rms=23.539 (2.093%) 018: dt: 0.0500, sse=15397157.0, rms=23.065 (2.014%) 019: dt: 0.0500, sse=14834374.0, rms=22.618 (1.938%) 020: dt: 0.0500, sse=14313804.0, rms=22.197 (1.864%) positioning took 1.7 minutes mean border=35.5, 58 (23) missing vertices, mean dist 1.1 [0.1 (%0.4)->1.8 (%99.6))] % 4 local maxima, %52 large gradients and %39 min vals, 488 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=14464558.0, rms=22.325 021: dt: 0.0500, sse=13975622.0, rms=21.924 (1.797%) 022: dt: 0.0500, sse=13521472.0, rms=21.545 (1.730%) 023: dt: 0.0500, sse=13097559.0, rms=21.185 (1.672%) 024: dt: 0.0500, sse=12702210.0, rms=20.843 (1.613%) 025: dt: 0.0500, sse=12332961.0, rms=20.519 (1.556%) 026: dt: 0.0500, sse=11986907.0, rms=20.210 (1.505%) 027: dt: 0.0500, sse=11659898.0, rms=19.913 (1.466%) 028: dt: 0.0500, sse=11348158.0, rms=19.627 (1.440%) 029: dt: 0.0500, sse=11051363.0, rms=19.350 (1.411%) 030: dt: 0.0500, sse=10767552.0, rms=19.081 (1.389%) positioning took 1.8 minutes mean border=35.4, 63 (17) missing vertices, mean dist 0.9 [0.1 (%6.4)->1.6 (%93.6))] % 5 local maxima, %52 large gradients and %39 min vals, 434 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=10865434.0, rms=19.175 031: dt: 0.5000, sse=8915426.0, rms=17.226 (10.164%) 032: dt: 0.5000, sse=7549577.5, rms=15.712 (8.788%) 033: dt: 0.5000, sse=6488172.0, rms=14.427 (8.177%) 034: dt: 0.5000, sse=5630940.5, rms=13.294 (7.854%) 035: dt: 0.5000, sse=4915899.0, rms=12.271 (7.697%) 036: dt: 0.5000, sse=4271905.5, rms=11.269 (8.167%) 037: dt: 0.5000, sse=3690490.0, rms=10.285 (8.733%) 038: dt: 0.5000, sse=3182030.0, rms=9.338 (9.208%) 039: dt: 0.5000, sse=2781255.8, rms=8.521 (8.745%) 040: dt: 0.5000, sse=2492529.0, rms=7.879 (7.542%) 041: dt: 0.5000, sse=2291382.2, rms=7.401 (6.068%) 042: dt: 0.5000, sse=2169662.2, rms=7.093 (4.161%) 043: dt: 0.5000, sse=2083813.0, rms=6.869 (3.147%) 044: dt: 0.5000, sse=2020463.4, rms=6.696 (2.518%) 045: dt: 0.5000, sse=1972177.8, rms=6.565 (1.962%) 046: dt: 0.5000, sse=1942087.2, rms=6.479 (1.314%) 047: dt: 0.5000, sse=1908906.8, rms=6.386 (1.424%) rms = 6.34, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=1893493.0, rms=6.340 (0.724%) 049: dt: 0.2500, sse=1739992.2, rms=5.844 (7.833%) 050: dt: 0.2500, sse=1692073.4, rms=5.693 (2.580%) rms = 5.70, time step reduction 2 of 3 to 0.125... 051: dt: 0.1250, sse=1677384.1, rms=5.643 (0.879%) 052: dt: 0.1250, sse=1658271.0, rms=5.576 (1.179%) rms = 5.57, time step reduction 3 of 3 to 0.062... 053: dt: 0.1250, sse=1656127.4, rms=5.568 (0.143%) positioning took 5.5 minutes mean border=34.6, 2179 (7) missing vertices, mean dist 0.1 [0.2 (%60.2)->0.6 (%39.8))] %10 local maxima, %46 large gradients and %39 min vals, 236 gradients ignored tol=1.0e-04, sigma=1.0, host= roxy, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=2000390.9, rms=5.790 054: dt: 0.5000, sse=1979889.6, rms=5.735 (0.959%) rms = 5.81, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1840044.8, rms=5.247 (8.511%) 056: dt: 0.2500, sse=1826371.1, rms=5.194 (1.006%) rms = 5.24, time step reduction 2 of 3 to 0.125... 057: dt: 0.1250, sse=1810930.6, rms=5.135 (1.132%) 058: dt: 0.1250, sse=1793155.6, rms=5.067 (1.337%) rms = 5.08, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1796001.6, rms=5.077 (-0.202%) positioning took 1.9 minutes mean border=34.0, 2544 (5) missing vertices, mean dist 0.1 [0.1 (%61.1)->0.5 (%38.9))] %27 local maxima, %28 large gradients and %38 min vals, 232 gradients ignored tol=1.0e-04, sigma=0.5, host= roxy, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1847721.0, rms=5.260 rms = 5.74, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1820146.6, rms=5.160 (1.897%) rms = 5.23, time step reduction 2 of 3 to 0.125... rms = 5.15, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1817593.6, rms=5.150 (0.197%) positioning took 0.9 minutes mean border=33.4, 5481 (5) missing vertices, mean dist 0.1 [0.1 (%54.1)->0.4 (%45.9))] %34 local maxima, %21 large gradients and %37 min vals, 266 gradients ignored tol=1.0e-04, sigma=0.2, host= roxy, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1828362.5, rms=5.185 rms = 5.18, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1774571.0, rms=4.991 (3.727%) 063: dt: 0.2500, sse=1709185.8, rms=4.762 (4.588%) 064: dt: 0.2500, sse=1677902.9, rms=4.654 (2.279%) 065: dt: 0.2500, sse=1654307.1, rms=4.575 (1.697%) rms = 4.55, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1646625.6, rms=4.551 (0.515%) 067: dt: 0.1250, sse=1599311.8, rms=4.351 (4.390%) rms = 4.31, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1587537.1, rms=4.306 (1.055%) positioning took 2.1 minutes writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.area.pial vertex spacing 1.07 +- 0.48 (0.07-->7.93) (max @ vno 96663 --> 95566) face area 0.44 +- 0.36 (0.00-->5.65) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 144528 vertices processed 25000 of 144528 vertices processed 50000 of 144528 vertices processed 75000 of 144528 vertices processed 100000 of 144528 vertices processed 125000 of 144528 vertices processed 0 of 144528 vertices processed 25000 of 144528 vertices processed 50000 of 144528 vertices processed 75000 of 144528 vertices processed 100000 of 144528 vertices processed 125000 of 144528 vertices processed thickness calculation complete, 540:3914 truncations. 32871 vertices at 0 distance 99564 vertices at 1 distance 90145 vertices at 2 distance 36932 vertices at 3 distance 11566 vertices at 4 distance 3259 vertices at 5 distance 968 vertices at 6 distance 313 vertices at 7 distance 134 vertices at 8 distance 68 vertices at 9 distance 59 vertices at 10 distance 41 vertices at 11 distance 50 vertices at 12 distance 27 vertices at 13 distance 32 vertices at 14 distance 26 vertices at 15 distance 21 vertices at 16 distance 25 vertices at 17 distance 29 vertices at 18 distance 16 vertices at 19 distance 20 vertices at 20 distance writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.thickness positioning took 28.6 minutes #-------------------------------------------- #@# Make Pial Surf rh Tue Jul 23 08:58:09 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs seg rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/filled.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/brain.finalsurfs.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/../mri/aseg.presurf.mgz... reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... 28879 bright wm thresholded. 1175 bright non-wm voxels segmented. reading original surface position from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.orig... computing class statistics... border white: 276765 voxels (1.65%) border gray 337536 voxels (2.01%) WM (99.0): 97.6 +- 10.4 [70.0 --> 110.0] GM (58.0) : 59.2 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 38.8 (was 70) setting MAX_BORDER_WHITE to 114.4 (was 105) setting MIN_BORDER_WHITE to 51.0 (was 85) setting MAX_CSF to 26.6 (was 40) setting MAX_GRAY to 93.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 38.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 14.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-5.2, GM=51+-9.6 mean inside = 91.6, mean outside = 63.6 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.24 (0.04-->4.59) (max @ vno 63968 --> 65291) face area 0.34 +- 0.15 (0.00-->4.01) mean absolute distance = 0.46 +- 0.65 3710 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown deleting segment 1 with 24 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 186 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 19 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown mean border=69.1, 114 (114) missing vertices, mean dist 0.3 [0.5 (%12.0)->0.5 (%88.0))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.11-->4.46) (max @ vno 63968 --> 65291) face area 0.34 +- 0.16 (0.00-->4.00) mean absolute distance = 0.28 +- 0.47 2933 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3760552.8, rms=10.415 001: dt: 0.5000, sse=1832335.2, rms=6.293 (39.581%) 002: dt: 0.5000, sse=1469495.6, rms=5.201 (17.341%) 003: dt: 0.5000, sse=1441228.9, rms=5.102 (1.910%) 004: dt: 0.5000, sse=1371893.1, rms=4.848 (4.983%) rms = 5.00, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=1001495.8, rms=3.191 (34.181%) 006: dt: 0.2500, sse=915621.9, rms=2.639 (17.286%) 007: dt: 0.2500, sse=873611.4, rms=2.357 (10.686%) rms = 2.38, time step reduction 2 of 3 to 0.125... 008: dt: 0.1250, sse=849295.4, rms=2.153 (8.650%) 009: dt: 0.1250, sse=814977.8, rms=1.846 (14.266%) 010: dt: 0.1250, sse=848649.2, rms=1.785 (3.301%) rms = 1.77, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=808143.3, rms=1.774 (0.606%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 14 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 59 points - only 0.00% unknown deleting segment 4 with 15 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=73.9, 66 (20) missing vertices, mean dist -0.2 [0.3 (%79.7)->0.2 (%20.3))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= roxy, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.09-->4.48) (max @ vno 63968 --> 65291) face area 0.36 +- 0.17 (0.00-->4.41) mean absolute distance = 0.19 +- 0.34 2698 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1890657.1, rms=6.329 012: dt: 0.5000, sse=1367272.8, rms=4.583 (27.594%) rms = 5.14, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=1032805.9, rms=3.073 (32.951%) 014: dt: 0.2500, sse=947534.4, rms=2.517 (18.094%) 015: dt: 0.2500, sse=905132.6, rms=2.208 (12.262%) rms = 2.26, time step reduction 2 of 3 to 0.125... 016: dt: 0.1250, sse=873878.7, rms=1.955 (11.473%) 017: dt: 0.1250, sse=836031.9, rms=1.559 (20.262%) 018: dt: 0.1250, sse=834256.8, rms=1.474 (5.443%) rms = 1.45, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=826178.6, rms=1.453 (1.412%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 16 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 71 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown mean border=76.7, 78 (12) missing vertices, mean dist -0.1 [0.2 (%72.0)->0.2 (%28.0))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= roxy, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.06-->4.52) (max @ vno 63968 --> 65291) face area 0.35 +- 0.16 (0.00-->4.12) mean absolute distance = 0.16 +- 0.28 2628 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1152318.6, rms=3.840 rms = 4.71, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=924022.7, rms=2.568 (33.133%) 021: dt: 0.2500, sse=830674.7, rms=1.769 (31.122%) 022: dt: 0.2500, sse=821708.5, rms=1.681 (4.971%) rms = 1.66, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=817093.4, rms=1.662 (1.102%) 024: dt: 0.1250, sse=790691.5, rms=1.339 (19.465%) 025: dt: 0.1250, sse=786967.1, rms=1.283 (4.180%) rms = 1.29, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=785391.6, rms=1.289 (-0.507%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 17 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 71 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown deleting segment 6 with 15 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown mean border=77.4, 101 (11) missing vertices, mean dist -0.0 [0.2 (%55.4)->0.2 (%44.6))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= roxy, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=819558.3, rms=1.764 rms = 3.09, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=767380.1, rms=1.151 (34.726%) 028: dt: 0.2500, sse=760623.5, rms=1.020 (11.417%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=758055.5, rms=0.996 (2.309%) positioning took 0.7 minutes generating cortex label... 4 non-cortical segments detected only using segment with 8155 vertices erasing segment 1 (vno[0] = 85654) erasing segment 2 (vno[0] = 104560) erasing segment 3 (vno[0] = 107492) writing cortex label to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.cortex.label... writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.curv writing smoothed area to rh.area writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.area vertex spacing 0.90 +- 0.25 (0.04-->4.54) (max @ vno 63968 --> 65291) face area 0.34 +- 0.16 (0.00-->4.06) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=36.5, 116 (116) missing vertices, mean dist 1.6 [0.9 (%0.0)->2.6 (%100.0))] % 5 local maxima, %53 large gradients and %38 min vals, 532 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=49512668.0, rms=41.693 001: dt: 0.0500, sse=43022064.0, rms=38.821 (6.888%) 002: dt: 0.0500, sse=38361540.0, rms=36.620 (5.669%) 003: dt: 0.0500, sse=34813036.0, rms=34.851 (4.831%) 004: dt: 0.0500, sse=31969982.0, rms=33.366 (4.261%) 005: dt: 0.0500, sse=29607138.0, rms=32.080 (3.856%) 006: dt: 0.0500, sse=27592906.0, rms=30.941 (3.550%) 007: dt: 0.0500, sse=25840002.0, rms=29.914 (3.318%) 008: dt: 0.0500, sse=24294240.0, rms=28.979 (3.127%) 009: dt: 0.0500, sse=22914372.0, rms=28.117 (2.972%) 010: dt: 0.0500, sse=21673470.0, rms=27.320 (2.838%) positioning took 1.5 minutes mean border=36.3, 108 (70) missing vertices, mean dist 1.3 [0.6 (%0.0)->2.1 (%100.0))] % 5 local maxima, %53 large gradients and %38 min vals, 517 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=22846744.0, rms=28.075 011: dt: 0.0500, sse=21718414.0, rms=27.350 (2.584%) 012: dt: 0.0500, sse=20691070.0, rms=26.672 (2.478%) 013: dt: 0.0500, sse=19752648.0, rms=26.037 (2.379%) 014: dt: 0.0500, sse=18892494.0, rms=25.442 (2.288%) 015: dt: 0.0500, sse=18103192.0, rms=24.883 (2.198%) 016: dt: 0.0500, sse=17376966.0, rms=24.357 (2.114%) 017: dt: 0.0500, sse=16708306.0, rms=23.862 (2.030%) 018: dt: 0.0500, sse=16091604.0, rms=23.397 (1.951%) 019: dt: 0.0500, sse=15521836.0, rms=22.958 (1.874%) 020: dt: 0.0500, sse=14995006.0, rms=22.545 (1.800%) positioning took 1.5 minutes mean border=36.2, 105 (52) missing vertices, mean dist 1.1 [0.1 (%0.6)->1.8 (%99.4))] % 5 local maxima, %52 large gradients and %38 min vals, 498 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=15156453.0, rms=22.677 021: dt: 0.0500, sse=14659814.0, rms=22.283 (1.738%) 022: dt: 0.0500, sse=14199162.0, rms=21.911 (1.670%) 023: dt: 0.0500, sse=13769045.0, rms=21.558 (1.612%) 024: dt: 0.0500, sse=13368527.0, rms=21.223 (1.551%) 025: dt: 0.0500, sse=12994805.0, rms=20.907 (1.493%) 026: dt: 0.0500, sse=12645368.0, rms=20.606 (1.439%) 027: dt: 0.0500, sse=12315425.0, rms=20.318 (1.398%) 028: dt: 0.0500, sse=12001166.0, rms=20.039 (1.370%) 029: dt: 0.0500, sse=11701850.0, rms=19.770 (1.342%) 030: dt: 0.0500, sse=11416417.0, rms=19.510 (1.315%) positioning took 1.5 minutes mean border=36.1, 141 (47) missing vertices, mean dist 0.9 [0.1 (%8.2)->1.6 (%91.8))] % 5 local maxima, %52 large gradients and %38 min vals, 413 gradients ignored tol=1.0e-04, sigma=2.0, host= roxy, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=11531047.0, rms=19.616 031: dt: 0.5000, sse=9573456.0, rms=17.742 (9.553%) 032: dt: 0.5000, sse=8184215.5, rms=16.276 (8.262%) 033: dt: 0.5000, sse=7034629.0, rms=14.957 (8.106%) 034: dt: 0.5000, sse=6023170.0, rms=13.687 (8.491%) 035: dt: 0.5000, sse=5143355.0, rms=12.479 (8.821%) 036: dt: 0.5000, sse=4370346.5, rms=11.311 (9.366%) 037: dt: 0.5000, sse=3697352.8, rms=10.189 (9.918%) 038: dt: 0.5000, sse=3138106.2, rms=9.150 (10.193%) 039: dt: 0.5000, sse=2727422.2, rms=8.309 (9.196%) 040: dt: 0.5000, sse=2441597.2, rms=7.666 (7.734%) 041: dt: 0.5000, sse=2257007.8, rms=7.224 (5.768%) 042: dt: 0.5000, sse=2145689.2, rms=6.940 (3.932%) 043: dt: 0.5000, sse=2070228.2, rms=6.744 (2.817%) 044: dt: 0.5000, sse=2018900.2, rms=6.604 (2.087%) 045: dt: 0.5000, sse=1979221.8, rms=6.496 (1.626%) 046: dt: 0.5000, sse=1952991.1, rms=6.421 (1.162%) 047: dt: 0.5000, sse=1930149.8, rms=6.357 (0.986%) 048: dt: 0.5000, sse=1910044.0, rms=6.300 (0.900%) rms = 6.26, time step reduction 1 of 3 to 0.250... 049: dt: 0.5000, sse=1896549.6, rms=6.262 (0.601%) 050: dt: 0.2500, sse=1734053.1, rms=5.737 (8.395%) 051: dt: 0.2500, sse=1675816.8, rms=5.554 (3.185%) rms = 5.58, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=1658673.4, rms=5.495 (1.054%) 053: dt: 0.1250, sse=1636792.5, rms=5.419 (1.393%) rms = 5.41, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1635851.4, rms=5.414 (0.083%) positioning took 6.4 minutes mean border=35.4, 2117 (11) missing vertices, mean dist 0.1 [0.2 (%60.3)->0.6 (%39.7))] %11 local maxima, %46 large gradients and %38 min vals, 179 gradients ignored tol=1.0e-04, sigma=1.0, host= roxy, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=2012441.8, rms=5.757 rms = 5.71, time step reduction 1 of 3 to 0.250... 055: dt: 0.5000, sse=1994469.5, rms=5.708 (0.847%) 056: dt: 0.2500, sse=1842980.0, rms=5.182 (9.216%) rms = 5.16, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1834392.6, rms=5.155 (0.512%) 058: dt: 0.1250, sse=1794959.5, rms=5.005 (2.926%) rms = 5.00, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1793337.0, rms=5.000 (0.097%) positioning took 1.5 minutes mean border=34.6, 2416 (6) missing vertices, mean dist 0.1 [0.1 (%59.5)->0.5 (%40.5))] %29 local maxima, %28 large gradients and %38 min vals, 197 gradients ignored tol=1.0e-04, sigma=0.5, host= roxy, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1876534.8, rms=5.292 rms = 5.76, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1843391.5, rms=5.175 (2.214%) rms = 5.20, time step reduction 2 of 3 to 0.125... rms = 5.16, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1839344.4, rms=5.160 (0.291%) positioning took 1.0 minutes mean border=33.9, 4940 (6) missing vertices, mean dist 0.1 [0.1 (%52.3)->0.4 (%47.7))] %35 local maxima, %21 large gradients and %36 min vals, 245 gradients ignored tol=1.0e-04, sigma=0.2, host= roxy, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1866857.4, rms=5.253 rms = 5.35, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1811230.8, rms=5.058 (3.717%) 063: dt: 0.2500, sse=1747453.8, rms=4.838 (4.333%) 064: dt: 0.2500, sse=1714798.8, rms=4.727 (2.314%) 065: dt: 0.2500, sse=1689161.6, rms=4.641 (1.817%) rms = 4.61, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1680129.6, rms=4.611 (0.640%) 067: dt: 0.1250, sse=1619860.6, rms=4.364 (5.349%) 068: dt: 0.1250, sse=1604300.4, rms=4.304 (1.387%) rms = 4.29, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1599558.5, rms=4.286 (0.403%) positioning took 2.7 minutes writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.area.pial vertex spacing 1.06 +- 0.47 (0.06-->7.36) (max @ vno 99094 --> 97837) face area 0.44 +- 0.35 (0.00-->6.01) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146765 vertices processed 25000 of 146765 vertices processed 50000 of 146765 vertices processed 75000 of 146765 vertices processed 100000 of 146765 vertices processed 125000 of 146765 vertices processed 0 of 146765 vertices processed 25000 of 146765 vertices processed 50000 of 146765 vertices processed 75000 of 146765 vertices processed 100000 of 146765 vertices processed 125000 of 146765 vertices processed thickness calculation complete, 587:3499 truncations. 34453 vertices at 0 distance 102278 vertices at 1 distance 90313 vertices at 2 distance 36745 vertices at 3 distance 11585 vertices at 4 distance 3334 vertices at 5 distance 1102 vertices at 6 distance 397 vertices at 7 distance 226 vertices at 8 distance 136 vertices at 9 distance 94 vertices at 10 distance 68 vertices at 11 distance 45 vertices at 12 distance 39 vertices at 13 distance 31 vertices at 14 distance 27 vertices at 15 distance 19 vertices at 16 distance 9 vertices at 17 distance 14 vertices at 18 distance 11 vertices at 19 distance 16 vertices at 20 distance writing curvature file /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.thickness positioning took 28.5 minutes #-------------------------------------------- #@# Surf Volume lh Tue Jul 23 09:26:40 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume seg lh /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.volume masking with /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.cortex.label Total face volume 296986 Total vertex volume 292823 (mask=0) #@# seg lh 292823 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue Jul 23 09:26:47 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume seg rh /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.volume masking with /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.cortex.label Total face volume 297352 Total vertex volume 292288 (mask=0) #@# seg rh 292288 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue Jul 23 09:26:55 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon seg SUBJECTS_DIR is /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 13 writing volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/ribbon.mgz mris_volmask took 23.82 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Tue Jul 23 09:50:44 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab seg lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 296986 Total vertex volume 292823 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1757 1243 3270 2.704 0.345 0.098 0.017 13 1.1 bankssts 751 483 1179 2.544 0.527 0.128 0.013 11 0.4 caudalanteriorcingulate 4211 2784 8373 2.615 0.585 0.113 0.021 40 3.6 caudalmiddlefrontal 1909 1360 3216 2.210 0.469 0.168 0.037 36 3.4 cuneus 572 386 2080 3.561 0.825 0.108 0.023 4 0.5 entorhinal 5076 3473 11042 2.800 0.708 0.126 0.026 75 5.2 fusiform 9096 6143 19097 2.440 0.691 0.122 0.022 120 8.1 inferiorparietal 5917 4218 16121 2.938 0.837 0.126 0.027 90 6.5 inferiortemporal 1782 1198 2857 2.102 0.744 0.138 0.029 31 2.2 isthmuscingulate 7839 5380 14435 2.238 0.695 0.149 0.030 121 9.7 lateraloccipital 4029 2785 8517 2.625 0.716 0.141 0.035 67 6.2 lateralorbitofrontal 3918 2754 7644 2.369 0.702 0.140 0.031 74 4.8 lingual 2860 2038 6556 2.878 0.741 0.136 0.031 50 3.5 medialorbitofrontal 5520 3828 17016 3.134 0.789 0.127 0.026 76 6.1 middletemporal 1046 651 2010 2.657 0.575 0.074 0.011 5 0.4 parahippocampal 2106 1428 4253 2.643 0.600 0.108 0.019 20 1.8 paracentral 2212 1522 5262 2.832 0.597 0.113 0.019 22 1.8 parsopercularis 1096 756 2938 2.650 0.840 0.137 0.028 20 1.2 parsorbitalis 1772 1210 4275 2.741 0.881 0.132 0.028 28 2.0 parstriangularis 1544 1081 2017 1.890 0.475 0.141 0.033 18 2.0 pericalcarine 6597 4355 11071 2.136 0.699 0.104 0.022 64 6.3 postcentral 1612 1126 2893 2.409 0.806 0.155 0.029 31 1.9 posteriorcingulate 9274 6051 19741 2.741 0.668 0.110 0.021 88 8.1 precentral 5504 3814 10380 2.563 0.524 0.127 0.024 65 5.5 precuneus 839 586 1894 3.006 0.577 0.131 0.026 14 0.9 rostralanteriorcingulate 9266 6370 19459 2.465 0.673 0.137 0.031 135 12.0 rostralmiddlefrontal 11456 7921 27414 2.885 0.626 0.129 0.026 132 12.0 superiorfrontal 9553 6349 17697 2.305 0.631 0.123 0.023 114 8.8 superiorparietal 6556 4406 17018 3.137 0.710 0.110 0.020 73 5.5 superiortemporal 5781 3905 11627 2.585 0.627 0.128 0.026 81 6.2 supramarginal 373 253 1251 3.040 0.716 0.158 0.033 9 0.6 frontalpole 651 517 2848 3.486 1.039 0.170 0.043 15 1.2 temporalpole 654 410 1064 2.485 0.455 0.121 0.018 9 0.4 transversetemporal 2819 1988 6302 2.940 0.803 0.120 0.028 29 3.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab seg lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 296986 Total vertex volume 292823 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1757 1161 3270 2.704 0.345 0.117 0.027 22 2.1 bankssts 751 525 1179 2.544 0.527 0.123 0.025 10 0.8 caudalanteriorcingulate 4211 3452 8373 2.615 0.585 0.132 0.026 52 5.4 caudalmiddlefrontal 1909 1642 3216 2.210 0.469 0.155 0.036 28 3.3 cuneus 572 772 2080 3.561 0.825 0.187 0.037 5 1.0 entorhinal 5076 4283 11042 2.800 0.708 0.151 0.037 95 8.7 fusiform 9096 8614 19097 2.440 0.691 0.160 0.033 146 14.4 inferiorparietal 5917 6406 16121 2.938 0.837 0.173 0.035 88 10.4 inferiortemporal 1782 1483 2857 2.102 0.744 0.147 0.036 31 2.8 isthmuscingulate 7839 7286 14435 2.238 0.695 0.161 0.035 133 13.7 lateraloccipital 4029 3538 8517 2.625 0.716 0.161 0.036 74 7.1 lateralorbitofrontal 3918 3754 7644 2.369 0.702 0.166 0.040 62 7.4 lingual 2860 2511 6556 2.878 0.741 0.154 0.037 46 4.6 medialorbitofrontal 5520 6378 17016 3.134 0.789 0.173 0.038 84 9.9 middletemporal 1046 912 2010 2.657 0.575 0.125 0.026 6 1.4 parahippocampal 2106 1795 4253 2.643 0.600 0.131 0.026 20 2.7 paracentral 2212 2107 5262 2.832 0.597 0.146 0.031 24 3.0 parsopercularis 1096 1324 2938 2.650 0.840 0.209 0.040 18 2.4 parsorbitalis 1772 1789 4275 2.741 0.881 0.169 0.039 24 3.5 parstriangularis 1544 1057 2017 1.890 0.475 0.137 0.037 31 2.3 pericalcarine 6597 5815 11071 2.136 0.699 0.133 0.026 67 8.1 postcentral 1612 1263 2893 2.409 0.806 0.151 0.052 66 2.5 posteriorcingulate 9274 7858 19741 2.741 0.668 0.129 0.027 106 11.5 precentral 5504 4347 10380 2.563 0.524 0.143 0.034 83 8.2 precuneus 839 766 1894 3.006 0.577 0.155 0.035 13 1.5 rostralanteriorcingulate 9266 8830 19459 2.465 0.673 0.173 0.037 136 16.8 rostralmiddlefrontal 11456 10479 27414 2.885 0.626 0.155 0.034 169 17.4 superiorfrontal 9553 8296 17697 2.305 0.631 0.149 0.031 137 13.8 superiorparietal 6556 6103 17018 3.137 0.710 0.149 0.033 77 10.1 superiortemporal 5781 4943 11627 2.585 0.627 0.150 0.033 90 8.9 supramarginal 373 534 1251 3.040 0.716 0.248 0.047 6 0.8 frontalpole 651 1057 2848 3.486 1.039 0.241 0.041 12 1.3 temporalpole 654 475 1064 2.485 0.455 0.119 0.031 6 0.9 transversetemporal 2819 2069 6302 2.940 0.803 0.145 0.037 50 4.3 insula #----------------------------------------- #@# Parcellation Stats rh Tue Jul 23 09:53:53 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab seg rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 297352 Total vertex volume 292288 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1651 1181 2885 2.570 0.389 0.099 0.013 10 1.0 bankssts 980 679 1957 2.749 0.834 0.125 0.018 14 0.9 caudalanteriorcingulate 3726 2559 8051 2.720 0.571 0.120 0.022 39 3.2 caudalmiddlefrontal 2043 1362 3011 2.078 0.487 0.158 0.040 39 3.2 cuneus 429 301 2042 3.839 0.781 0.093 0.018 4 0.3 entorhinal 4237 2982 10480 2.958 0.685 0.131 0.028 59 5.3 fusiform 8820 5993 20027 2.567 0.674 0.122 0.022 112 7.9 inferiorparietal 5317 3613 13119 2.889 0.813 0.121 0.024 64 5.5 inferiortemporal 1681 1122 3034 2.439 0.806 0.135 0.027 29 1.7 isthmuscingulate 8199 5581 15462 2.363 0.641 0.141 0.030 116 10.2 lateraloccipital 4225 2895 9161 2.711 0.782 0.131 0.034 61 6.1 lateralorbitofrontal 4749 3365 9020 2.395 0.694 0.158 0.037 80 7.8 lingual 2856 2024 6009 2.540 0.787 0.122 0.024 49 2.7 medialorbitofrontal 6347 4480 18972 3.070 0.854 0.132 0.025 95 7.1 middletemporal 1217 760 2292 2.643 0.704 0.082 0.012 7 0.6 parahippocampal 2126 1383 3995 2.699 0.542 0.111 0.023 18 2.0 paracentral 1834 1252 3977 2.766 0.611 0.102 0.021 18 1.4 parsopercularis 1355 932 3490 2.712 0.785 0.144 0.035 26 1.8 parsorbitalis 2216 1543 4995 2.695 0.679 0.121 0.022 25 2.1 parstriangularis 1641 1189 2266 1.986 0.474 0.143 0.031 22 2.1 pericalcarine 7191 4661 11966 2.200 0.720 0.115 0.030 91 9.2 postcentral 1743 1213 3297 2.494 0.666 0.139 0.021 30 1.6 posteriorcingulate 7885 5171 17184 2.754 0.668 0.103 0.020 60 6.5 precentral 6674 4597 12278 2.535 0.527 0.131 0.026 82 7.5 precuneus 1085 739 2477 2.780 0.657 0.135 0.029 21 1.3 rostralanteriorcingulate 11460 7978 23643 2.413 0.689 0.135 0.028 183 12.9 rostralmiddlefrontal 10072 6797 22654 2.800 0.686 0.122 0.024 106 9.6 superiorfrontal 9293 6150 15369 2.181 0.518 0.120 0.021 112 7.9 superiorparietal 6434 4396 15454 2.917 0.709 0.117 0.023 80 6.2 superiortemporal 5867 3960 11247 2.517 0.592 0.119 0.021 63 5.3 supramarginal 493 332 1559 3.123 0.682 0.151 0.036 9 0.8 frontalpole 508 370 2648 4.108 0.688 0.131 0.035 7 0.8 temporalpole 538 358 1001 2.545 0.415 0.117 0.015 6 0.3 transversetemporal 3076 2171 7232 3.129 0.837 0.117 0.028 29 3.4 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab seg rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 297352 Total vertex volume 292288 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1651 1054 2885 2.570 0.389 0.104 0.026 27 1.7 bankssts 980 791 1957 2.749 0.834 0.151 0.038 56 1.5 caudalanteriorcingulate 3726 3198 8051 2.720 0.571 0.132 0.027 41 4.7 caudalmiddlefrontal 2043 1600 3011 2.078 0.487 0.147 0.036 37 3.5 cuneus 429 706 2042 3.839 0.781 0.245 0.048 4 1.2 entorhinal 4237 3996 10480 2.958 0.685 0.163 0.039 85 7.8 fusiform 8820 8453 20027 2.567 0.674 0.153 0.030 111 12.7 inferiorparietal 5317 5230 13119 2.889 0.813 0.164 0.037 78 10.1 inferiortemporal 1681 1321 3034 2.439 0.806 0.135 0.035 32 2.6 isthmuscingulate 8199 7336 15462 2.363 0.641 0.157 0.037 131 14.6 lateraloccipital 4225 3694 9161 2.711 0.782 0.160 0.037 69 7.6 lateralorbitofrontal 4749 4249 9020 2.395 0.694 0.163 0.040 87 8.6 lingual 2856 2623 6009 2.540 0.787 0.148 0.032 34 4.1 medialorbitofrontal 6347 7422 18972 3.070 0.854 0.178 0.036 81 11.1 middletemporal 1217 1019 2292 2.643 0.704 0.139 0.032 13 1.9 parahippocampal 2126 1583 3995 2.699 0.542 0.122 0.027 27 2.4 paracentral 1834 1587 3977 2.766 0.611 0.124 0.025 17 2.1 parsopercularis 1355 1592 3490 2.712 0.785 0.204 0.042 22 2.9 parsorbitalis 2216 2112 4995 2.695 0.679 0.153 0.031 31 3.2 parstriangularis 1641 1170 2266 1.986 0.474 0.139 0.031 37 2.2 pericalcarine 7191 6088 11966 2.200 0.720 0.137 0.031 86 10.0 postcentral 1743 1398 3297 2.494 0.666 0.151 0.036 46 3.0 posteriorcingulate 7885 6691 17184 2.754 0.668 0.127 0.027 91 9.5 precentral 6674 5087 12278 2.535 0.527 0.135 0.030 95 8.9 precuneus 1085 1073 2477 2.780 0.657 0.186 0.039 25 1.8 rostralanteriorcingulate 11460 10904 23643 2.413 0.689 0.166 0.033 171 18.6 rostralmiddlefrontal 10072 8735 22654 2.800 0.686 0.145 0.031 139 13.9 superiorfrontal 9293 7768 15369 2.181 0.518 0.145 0.027 123 11.6 superiorparietal 6434 6034 15454 2.917 0.709 0.154 0.035 80 10.3 superiortemporal 5867 4762 11247 2.517 0.592 0.134 0.030 71 7.9 supramarginal 493 635 1559 3.123 0.682 0.216 0.045 6 0.9 frontalpole 508 841 2648 4.108 0.688 0.213 0.038 5 1.0 temporalpole 538 427 1001 2.545 0.415 0.132 0.030 9 0.7 transversetemporal 3076 2173 7232 3.129 0.837 0.140 0.045 70 6.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Jul 23 09:56:45 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 seg lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 40 labels changed using aseg relabeling using gibbs priors... 000: 9770 changed, 144528 examined... 001: 2208 changed, 37608 examined... 002: 668 changed, 11779 examined... 003: 270 changed, 3772 examined... 004: 141 changed, 1542 examined... 005: 62 changed, 818 examined... 006: 30 changed, 369 examined... 007: 23 changed, 173 examined... 008: 9 changed, 136 examined... 009: 2 changed, 43 examined... 010: 4 changed, 24 examined... 011: 0 changed, 16 examined... 24 labels changed using aseg 000: 284 total segments, 193 labels (2020 vertices) changed 001: 99 total segments, 9 labels (72 vertices) changed 002: 90 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1015 vertices marked for relabeling... 1015 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 35 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Tue Jul 23 09:57:20 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 seg rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 25 labels changed using aseg relabeling using gibbs priors... 000: 9630 changed, 146765 examined... 001: 2208 changed, 37819 examined... 002: 615 changed, 11562 examined... 003: 246 changed, 3557 examined... 004: 126 changed, 1397 examined... 005: 68 changed, 700 examined... 006: 35 changed, 401 examined... 007: 16 changed, 208 examined... 008: 10 changed, 92 examined... 009: 5 changed, 52 examined... 010: 2 changed, 29 examined... 011: 1 changed, 14 examined... 012: 2 changed, 7 examined... 013: 2 changed, 12 examined... 014: 1 changed, 12 examined... 015: 0 changed, 7 examined... 19 labels changed using aseg 000: 260 total segments, 173 labels (3113 vertices) changed 001: 100 total segments, 13 labels (71 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 44 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 824 vertices marked for relabeling... 824 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 39 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Jul 23 09:57:59 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab seg lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 296986 Total vertex volume 292823 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1286 907 2913 2.557 0.773 0.146 0.031 20 1.7 G&S_frontomargin 1951 1333 3936 2.402 0.727 0.150 0.029 35 2.5 G&S_occipital_inf 1576 1033 3763 2.733 0.738 0.114 0.020 17 1.3 G&S_paracentral 1401 962 3739 2.908 0.713 0.130 0.028 17 1.7 G&S_subcentral 714 492 1913 2.862 0.562 0.167 0.036 16 1.2 G&S_transv_frontopol 2121 1493 4354 2.768 0.490 0.118 0.024 27 1.9 G&S_cingul-Ant 1262 870 2157 2.464 0.473 0.112 0.016 10 0.8 G&S_cingul-Mid-Ant 1317 958 2547 2.524 0.623 0.145 0.029 23 1.6 G&S_cingul-Mid-Post 627 490 1702 2.902 0.598 0.180 0.042 13 1.2 G_cingul-Post-dorsal 386 255 683 2.275 0.643 0.147 0.029 7 0.4 G_cingul-Post-ventral 1724 1246 3165 2.219 0.487 0.170 0.038 34 3.1 G_cuneus 1269 861 3821 3.068 0.512 0.115 0.020 17 1.1 G_front_inf-Opercular 347 233 1222 3.263 0.639 0.163 0.037 7 0.5 G_front_inf-Orbital 1052 705 3401 3.223 0.801 0.154 0.039 25 1.5 G_front_inf-Triangul 5288 3493 13681 2.752 0.670 0.145 0.033 96 7.5 G_front_middle 7818 5356 21550 3.102 0.591 0.139 0.030 108 9.5 G_front_sup 493 376 1576 3.517 0.985 0.112 0.022 4 0.3 G_Ins_lg&S_cent_ins 684 480 2213 3.340 0.643 0.144 0.038 13 1.2 G_insular_short 2587 1756 6993 2.666 0.721 0.146 0.030 49 3.0 G_occipital_middle 1460 968 3031 2.344 0.720 0.135 0.024 21 1.5 G_occipital_sup 2018 1354 5371 2.972 0.595 0.145 0.031 45 2.5 G_oc-temp_lat-fusifor 2907 2040 6331 2.467 0.760 0.151 0.037 68 4.1 G_oc-temp_med-Lingual 1302 837 3606 3.124 0.784 0.096 0.018 9 0.8 G_oc-temp_med-Parahip 2532 1744 7100 2.892 0.739 0.148 0.040 56 4.2 G_orbital 3425 2289 10084 2.859 0.767 0.136 0.029 68 4.0 G_pariet_inf-Angular 2603 1795 6494 2.822 0.631 0.143 0.030 49 3.0 G_pariet_inf-Supramar 3572 2345 8627 2.596 0.705 0.136 0.027 58 3.9 G_parietal_sup 2529 1601 4635 2.225 0.630 0.113 0.030 35 3.4 G_postcentral 3778 2405 10164 3.075 0.675 0.120 0.026 47 4.1 G_precentral 2773 1953 6821 2.692 0.549 0.148 0.032 48 3.8 G_precuneus 1005 761 3106 3.062 0.748 0.166 0.039 31 1.9 G_rectus 579 345 1131 3.175 0.804 0.092 0.030 5 0.6 G_subcallosal 422 255 836 2.688 0.353 0.106 0.016 6 0.2 G_temp_sup-G_T_transv 2318 1584 8698 3.642 0.647 0.153 0.033 46 3.1 G_temp_sup-Lateral 733 524 2237 3.389 0.631 0.068 0.009 2 0.2 G_temp_sup-Plan_polar 1149 778 2677 2.942 0.575 0.122 0.025 15 1.4 G_temp_sup-Plan_tempo 3312 2321 11232 3.263 0.836 0.134 0.030 60 4.5 G_temporal_inf 2977 2088 11634 3.392 0.823 0.136 0.032 53 3.9 G_temporal_middle 339 223 446 1.926 0.584 0.091 0.014 1 0.1 Lat_Fis-ant-Horizont 374 263 629 2.630 0.508 0.099 0.016 2 0.2 Lat_Fis-ant-Vertical 917 611 1218 2.475 0.394 0.112 0.023 7 0.8 Lat_Fis-post 2332 1580 3721 1.994 0.709 0.162 0.038 40 3.8 Pole_occipital 1567 1193 5686 3.203 0.929 0.156 0.040 33 2.5 Pole_temporal 1758 1225 2202 1.980 0.473 0.118 0.022 15 1.6 S_calcarine 3493 2335 4447 2.088 0.625 0.091 0.015 15 2.1 S_central 990 693 1370 2.177 0.381 0.089 0.011 4 0.5 S_cingul-Marginalis 464 312 773 2.809 0.345 0.091 0.015 2 0.3 S_circular_insula_ant 1381 889 1988 2.546 0.754 0.084 0.015 6 1.0 S_circular_insula_inf 1476 1003 2088 2.491 0.373 0.095 0.016 6 1.0 S_circular_insula_sup 1173 844 3024 3.125 0.897 0.115 0.033 20 1.0 S_collat_transv_ant 491 341 819 2.297 0.662 0.159 0.032 7 0.7 S_collat_transv_post 2085 1464 3315 2.332 0.471 0.115 0.020 16 1.8 S_front_inf 2015 1376 2771 2.074 0.484 0.108 0.022 13 1.7 S_front_middle 3543 2496 6407 2.431 0.525 0.113 0.020 30 2.9 S_front_sup 270 196 537 3.016 0.564 0.141 0.031 2 0.5 S_interm_prim-Jensen 4109 2722 4869 1.963 0.356 0.111 0.017 36 3.0 S_intrapariet&P_trans 1037 728 1395 2.076 0.348 0.135 0.027 9 1.2 S_oc_middle&Lunatus 1479 1009 1961 2.085 0.382 0.117 0.020 13 1.2 S_oc_sup&transversal 510 339 591 2.002 0.407 0.105 0.016 3 0.3 S_occipital_ant 1474 1039 2244 2.260 0.590 0.112 0.017 11 1.0 S_oc-temp_lat 1993 1377 2906 2.337 0.404 0.095 0.013 11 1.1 S_oc-temp_med&Lingual 392 277 758 2.432 0.697 0.128 0.021 5 0.4 S_orbital_lateral 690 486 984 2.208 0.619 0.114 0.014 5 0.3 S_orbital_med-olfact 1569 1099 2543 2.197 0.618 0.146 0.036 23 2.6 S_orbital-H_Shaped 1771 1207 2540 2.315 0.405 0.113 0.020 15 1.5 S_parieto_occipital 1316 745 991 1.861 0.846 0.129 0.016 25 0.8 S_pericallosal 3488 2330 4836 2.080 0.443 0.100 0.017 25 2.3 S_postcentral 1975 1318 2843 2.404 0.377 0.102 0.016 12 1.3 S_precentral-inf-part 1861 1256 2842 2.348 0.476 0.105 0.021 13 1.5 S_precentral-sup-part 609 443 1135 2.831 0.685 0.140 0.022 6 0.5 S_suborbital 1496 1022 2276 2.590 0.468 0.120 0.024 11 1.5 S_subparietal 1961 1340 3021 2.623 0.444 0.112 0.018 14 1.5 S_temporal_inf 7840 5418 12787 2.484 0.479 0.102 0.016 59 5.1 S_temporal_sup 411 288 718 2.629 0.386 0.126 0.016 3 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Tue Jul 23 09:59:27 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab seg rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 297352 Total vertex volume 292288 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1108 790 2146 2.245 0.642 0.144 0.025 19 1.2 G&S_frontomargin 1235 823 2768 2.773 0.656 0.131 0.027 17 1.3 G&S_occipital_inf 1501 930 2882 2.462 0.512 0.122 0.029 17 1.7 G&S_paracentral 1710 1160 4302 2.855 0.669 0.125 0.030 27 2.4 G&S_subcentral 1222 880 3288 2.708 0.676 0.158 0.036 29 2.0 G&S_transv_frontopol 3113 2174 5984 2.489 0.709 0.119 0.025 39 3.0 G&S_cingul-Ant 1280 904 2405 2.611 0.451 0.115 0.019 15 1.2 G&S_cingul-Mid-Ant 1366 961 2738 2.714 0.505 0.118 0.020 13 1.1 G&S_cingul-Mid-Post 640 455 1678 2.851 0.632 0.172 0.035 15 1.0 G_cingul-Post-dorsal 360 251 856 2.734 0.715 0.152 0.035 6 0.5 G_cingul-Post-ventral 1917 1308 2998 2.067 0.506 0.160 0.042 38 3.1 G_cuneus 1227 845 3320 3.007 0.597 0.120 0.026 18 1.2 G_front_inf-Opercular 510 348 1311 2.805 0.498 0.130 0.027 10 0.6 G_front_inf-Orbital 826 566 2515 3.069 0.770 0.135 0.027 15 0.8 G_front_inf-Triangul 5295 3569 14162 2.810 0.688 0.145 0.032 104 6.6 G_front_middle 6514 4345 17992 3.109 0.609 0.134 0.028 90 7.5 G_front_sup 555 417 1677 3.636 0.708 0.146 0.060 11 1.5 G_Ins_lg&S_cent_ins 569 405 2232 3.765 0.659 0.134 0.030 8 0.8 G_insular_short 3305 2163 8846 2.773 0.684 0.130 0.023 49 3.3 G_occipital_middle 1718 1174 3425 2.180 0.649 0.139 0.026 27 1.9 G_occipital_sup 1974 1392 6398 3.217 0.639 0.158 0.037 46 3.5 G_oc-temp_lat-fusifor 2952 2131 6282 2.360 0.771 0.169 0.042 60 5.3 G_oc-temp_med-Lingual 1260 786 3941 3.174 0.919 0.089 0.016 9 0.8 G_oc-temp_med-Parahip 3075 2131 8945 2.964 0.830 0.151 0.047 68 5.5 G_orbital 2870 1915 8216 2.757 0.771 0.141 0.029 56 3.4 G_pariet_inf-Angular 2898 1952 5989 2.561 0.627 0.126 0.023 37 2.7 G_pariet_inf-Supramar 2940 1878 6004 2.380 0.565 0.128 0.026 48 2.9 G_parietal_sup 2654 1560 4605 2.244 0.715 0.129 0.047 49 5.1 G_postcentral 2992 1896 9073 3.158 0.630 0.106 0.024 29 2.9 G_precentral 3099 2131 7055 2.799 0.442 0.154 0.034 54 4.3 G_precuneus 738 542 2000 2.784 0.591 0.125 0.024 19 0.8 G_rectus 277 196 799 3.372 0.718 0.134 0.034 6 0.3 G_subcallosal 389 259 889 2.731 0.422 0.131 0.018 6 0.3 G_temp_sup-G_T_transv 2294 1598 7441 3.214 0.829 0.143 0.034 39 3.3 G_temp_sup-Lateral 758 540 1911 3.122 0.920 0.097 0.021 6 0.6 G_temp_sup-Plan_polar 1196 792 2856 2.847 0.692 0.126 0.025 19 1.1 G_temp_sup-Plan_tempo 2711 1871 8691 3.198 0.821 0.130 0.028 44 3.3 G_temporal_inf 3711 2590 13319 3.332 0.861 0.142 0.030 70 4.8 G_temporal_middle 366 257 639 2.602 0.356 0.116 0.013 4 0.2 Lat_Fis-ant-Horizont 182 127 277 2.415 0.464 0.111 0.020 1 0.2 Lat_Fis-ant-Vertical 1436 970 2147 2.483 0.439 0.105 0.017 11 1.0 Lat_Fis-post 3418 2335 5910 2.206 0.620 0.162 0.040 62 6.0 Pole_occipital 1693 1199 6521 3.482 0.862 0.134 0.030 23 2.1 Pole_temporal 1969 1393 2568 2.069 0.457 0.127 0.028 21 2.5 S_calcarine 3417 2325 4129 2.019 0.610 0.091 0.014 17 2.0 S_central 1301 877 1960 2.324 0.419 0.100 0.016 7 0.9 S_cingul-Marginalis 701 466 1050 2.767 0.824 0.102 0.015 4 0.4 S_circular_insula_ant 1255 815 2051 2.747 0.633 0.066 0.009 3 0.4 S_circular_insula_inf 1324 928 2083 2.639 0.526 0.100 0.016 6 0.9 S_circular_insula_sup 898 617 1924 2.902 0.763 0.107 0.021 6 0.8 S_collat_transv_ant 386 263 545 2.377 0.460 0.141 0.024 4 0.5 S_collat_transv_post 2268 1653 3816 2.288 0.418 0.097 0.014 16 1.4 S_front_inf 3551 2472 5532 2.130 0.590 0.117 0.020 30 2.9 S_front_middle 3132 2156 5128 2.339 0.541 0.116 0.024 27 2.8 S_front_sup 532 353 630 2.250 0.341 0.121 0.022 5 0.5 S_interm_prim-Jensen 4059 2773 5475 2.077 0.392 0.108 0.017 29 2.8 S_intrapariet&P_trans 1328 931 1651 2.034 0.390 0.123 0.023 10 1.4 S_oc_middle&Lunatus 1766 1187 2425 2.163 0.365 0.116 0.019 14 1.2 S_oc_sup&transversal 1080 751 1529 2.430 0.349 0.125 0.024 9 1.0 S_occipital_ant 1221 820 1855 2.490 0.429 0.102 0.019 7 0.9 S_oc-temp_lat 2200 1563 3342 2.502 0.538 0.103 0.016 13 1.4 S_oc-temp_med&Lingual 511 367 654 2.055 0.313 0.122 0.021 4 0.4 S_orbital_lateral 878 605 1278 2.298 0.643 0.101 0.013 6 0.4 S_orbital_med-olfact 1542 1071 2890 2.509 0.710 0.137 0.030 18 2.0 S_orbital-H_Shaped 2035 1351 2684 2.192 0.490 0.108 0.017 16 1.4 S_parieto_occipital 1607 995 1583 2.171 0.895 0.126 0.015 26 0.8 S_pericallosal 2800 1924 4028 2.161 0.492 0.115 0.020 26 2.3 S_postcentral 1845 1253 2874 2.500 0.438 0.092 0.013 11 0.9 S_precentral-inf-part 1452 964 2077 2.408 0.467 0.107 0.020 9 1.2 S_precentral-sup-part 226 148 404 3.088 0.879 0.108 0.021 1 0.2 S_suborbital 2045 1425 3469 2.498 0.527 0.117 0.020 20 1.8 S_subparietal 1727 1187 2277 2.330 0.478 0.118 0.019 13 1.5 S_temporal_inf 6802 4761 12498 2.580 0.486 0.107 0.016 55 4.7 S_temporal_sup 254 176 446 2.626 0.481 0.109 0.014 1 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Jul 23 10:00:55 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 seg lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1840 labels changed using aseg relabeling using gibbs priors... 000: 2199 changed, 144528 examined... 001: 533 changed, 9975 examined... 002: 168 changed, 2979 examined... 003: 63 changed, 947 examined... 004: 38 changed, 343 examined... 005: 29 changed, 236 examined... 006: 18 changed, 157 examined... 007: 16 changed, 115 examined... 008: 11 changed, 95 examined... 009: 6 changed, 59 examined... 010: 5 changed, 38 examined... 011: 4 changed, 29 examined... 012: 2 changed, 25 examined... 013: 3 changed, 15 examined... 014: 4 changed, 21 examined... 015: 5 changed, 22 examined... 016: 2 changed, 26 examined... 017: 1 changed, 10 examined... 018: 1 changed, 7 examined... 019: 3 changed, 7 examined... 020: 2 changed, 13 examined... 021: 2 changed, 15 examined... 022: 3 changed, 12 examined... 023: 5 changed, 17 examined... 024: 4 changed, 24 examined... 025: 2 changed, 17 examined... 026: 4 changed, 15 examined... 027: 1 changed, 20 examined... 028: 0 changed, 7 examined... 390 labels changed using aseg 000: 62 total segments, 29 labels (247 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 639 vertices marked for relabeling... 639 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 31 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Tue Jul 23 10:01:26 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 seg rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1853 labels changed using aseg relabeling using gibbs priors... 000: 2108 changed, 146765 examined... 001: 488 changed, 9869 examined... 002: 142 changed, 2713 examined... 003: 63 changed, 809 examined... 004: 37 changed, 367 examined... 005: 20 changed, 208 examined... 006: 15 changed, 109 examined... 007: 10 changed, 95 examined... 008: 5 changed, 58 examined... 009: 4 changed, 26 examined... 010: 1 changed, 19 examined... 011: 0 changed, 8 examined... 325 labels changed using aseg 000: 68 total segments, 35 labels (715 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 362 vertices marked for relabeling... 362 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 36 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Jul 23 10:02:01 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab seg lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 296986 Total vertex volume 292823 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1542 1026 2904 2.643 0.486 0.127 0.018 20 1.0 caudalanteriorcingulate 4643 3069 8976 2.590 0.571 0.113 0.021 45 4.0 caudalmiddlefrontal 2552 1796 4269 2.211 0.451 0.151 0.033 41 3.8 cuneus 557 372 1977 3.555 0.801 0.106 0.022 4 0.5 entorhinal 4565 3110 9845 2.787 0.721 0.129 0.026 70 4.6 fusiform 9171 6173 19560 2.453 0.708 0.123 0.023 124 8.4 inferiorparietal 6077 4357 17157 2.985 0.840 0.128 0.028 96 7.0 inferiortemporal 1759 1181 2838 2.127 0.745 0.140 0.028 31 2.3 isthmuscingulate 7739 5288 14147 2.231 0.673 0.147 0.029 117 9.4 lateraloccipital 4508 3121 10346 2.720 0.792 0.145 0.037 80 7.2 lateralorbitofrontal 4056 2870 7799 2.341 0.702 0.142 0.031 77 5.0 lingual 2140 1559 5404 2.948 0.805 0.141 0.031 41 2.8 medialorbitofrontal 7311 5062 19920 2.984 0.764 0.119 0.023 89 7.1 middletemporal 1109 688 2107 2.646 0.567 0.074 0.011 6 0.4 parahippocampal 2415 1648 5005 2.672 0.615 0.108 0.020 21 1.9 paracentral 1985 1368 4642 2.813 0.575 0.111 0.018 19 1.5 parsopercularis 974 664 2431 2.748 0.766 0.129 0.024 13 0.9 parsorbitalis 2181 1506 5182 2.730 0.857 0.132 0.028 33 2.6 parstriangularis 1546 1083 2016 1.878 0.458 0.141 0.032 18 2.0 pericalcarine 7355 4882 12524 2.170 0.711 0.106 0.022 73 6.9 postcentral 1756 1233 3175 2.416 0.800 0.152 0.029 33 2.1 posteriorcingulate 8967 5853 19144 2.744 0.673 0.109 0.021 84 7.6 precentral 5498 3807 10664 2.572 0.525 0.130 0.025 70 5.7 precuneus 1392 969 2862 2.880 0.584 0.129 0.025 20 1.4 rostralanteriorcingulate 7013 4796 15274 2.483 0.686 0.139 0.031 107 9.3 rostralmiddlefrontal 12470 8593 29025 2.810 0.656 0.130 0.027 152 13.8 superiorfrontal 7980 5288 14679 2.302 0.628 0.121 0.023 93 7.3 superiorparietal 8315 5712 21920 3.107 0.731 0.114 0.022 97 7.4 superiortemporal 5332 3607 10450 2.567 0.620 0.130 0.027 74 5.9 supramarginal 660 415 1076 2.491 0.447 0.124 0.019 9 0.4 transversetemporal 2378 1675 5505 2.945 0.774 0.119 0.027 25 2.8 insula #----------------------------------------- #@# Parcellation Stats 3 rh Tue Jul 23 10:03:32 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab seg rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 297352 Total vertex volume 292288 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1050 725 2048 2.685 0.833 0.127 0.019 15 0.9 caudalanteriorcingulate 3999 2737 8618 2.723 0.576 0.122 0.023 47 3.6 caudalmiddlefrontal 2530 1717 3842 2.088 0.466 0.147 0.036 43 3.5 cuneus 418 295 2062 3.872 0.792 0.100 0.019 4 0.3 entorhinal 3924 2769 9578 2.926 0.668 0.131 0.028 55 4.9 fusiform 9085 6153 20608 2.570 0.689 0.124 0.022 115 8.3 inferiorparietal 5613 3822 14203 2.934 0.818 0.122 0.025 68 5.9 inferiortemporal 1681 1126 3071 2.442 0.789 0.134 0.027 29 1.7 isthmuscingulate 8322 5654 15658 2.345 0.641 0.142 0.030 123 10.5 lateraloccipital 4726 3259 10570 2.708 0.808 0.137 0.038 76 7.6 lateralorbitofrontal 4651 3304 8817 2.390 0.691 0.157 0.037 77 7.7 lingual 2115 1507 4950 2.727 0.768 0.124 0.025 41 2.2 medialorbitofrontal 7424 5249 20832 3.003 0.824 0.128 0.024 101 7.7 middletemporal 1248 773 2345 2.656 0.711 0.080 0.012 7 0.6 parahippocampal 2199 1430 4265 2.714 0.538 0.115 0.024 21 2.1 paracentral 2142 1468 4686 2.770 0.593 0.105 0.021 22 1.5 parsopercularis 1269 845 2810 2.581 0.789 0.121 0.023 14 1.2 parsorbitalis 2054 1448 4428 2.613 0.696 0.120 0.021 24 1.8 parstriangularis 1657 1187 2287 1.999 0.499 0.141 0.031 21 2.1 pericalcarine 7813 5087 12807 2.189 0.705 0.117 0.030 100 9.8 postcentral 1869 1300 3584 2.512 0.651 0.138 0.022 32 1.8 posteriorcingulate 7610 4979 16899 2.768 0.669 0.103 0.020 60 6.3 precentral 6923 4740 12761 2.523 0.535 0.132 0.026 88 7.9 precuneus 1347 919 2891 2.731 0.696 0.133 0.028 24 1.5 rostralanteriorcingulate 8566 5940 18247 2.450 0.696 0.135 0.028 132 9.4 rostralmiddlefrontal 13298 9052 28819 2.685 0.719 0.124 0.025 159 13.1 superiorfrontal 7610 5055 12803 2.201 0.519 0.117 0.020 86 6.1 superiorparietal 8035 5516 19853 2.941 0.745 0.117 0.024 96 7.7 superiortemporal 5529 3719 10221 2.490 0.569 0.117 0.022 58 4.8 supramarginal 527 347 986 2.554 0.407 0.114 0.015 6 0.3 transversetemporal 2732 1962 6740 3.182 0.806 0.114 0.024 24 2.6 insula #----------------------------------------- #@# WM/GM Contrast lh Tue Jul 23 10:04:57 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts pctsurfcon --s seg --lh-only Log file is /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts/pctsurfcon.log Tue Jul 23 10:04:57 EDT 2019 setenv SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 cd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux roxy 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54472/lh.wm.mgh --regheader seg --cortex srcvol = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.cortex.label Reading surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 83615 Masking with /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.cortex.label Writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54472/lh.wm.mgh Dim: 144528 1 1 mri_vol2surf --mov /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54472/lh.gm.mgh --projfrac 0.3 --regheader seg --cortex srcvol = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.cortex.label Reading surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Done reading source surface Reading thickness /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 98579 Masking with /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.cortex.label Writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54472/lh.gm.mgh Dim: 144528 1 1 mri_concat /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54472/lh.wm.mgh /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54472/lh.gm.mgh --paired-diff-norm --mul 100 --o /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.w-g.pct.mgh mri_segstats --in /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.w-g.pct.mgh --annot seg lh aparc --sum /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.w-g.pct.mgh --annot seg lh aparc --sum /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/stats/lh.w-g.pct.stats --snr sysname Linux hostname roxy machine x86_64 user pkashyap UseRobust 0 Constructing seg from annotation Reading annotation /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.w-g.pct.mgh Vertex Area is 0.681283 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Tue Jul 23 10:05:07 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts pctsurfcon --s seg --rh-only Log file is /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts/pctsurfcon.log Tue Jul 23 10:05:07 EDT 2019 setenv SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 cd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux roxy 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54938/rh.wm.mgh --regheader seg --cortex srcvol = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.cortex.label Reading surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 84732 Masking with /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.cortex.label Writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54938/rh.wm.mgh Dim: 146765 1 1 mri_vol2surf --mov /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54938/rh.gm.mgh --projfrac 0.3 --regheader seg --cortex srcvol = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.cortex.label Reading surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Done reading source surface Reading thickness /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 100078 Masking with /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.cortex.label Writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54938/rh.gm.mgh Dim: 146765 1 1 mri_concat /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54938/rh.wm.mgh /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/tmp.pctsurfcon.54938/rh.gm.mgh --paired-diff-norm --mul 100 --o /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.w-g.pct.mgh mri_segstats --in /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.w-g.pct.mgh --annot seg rh aparc --sum /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.w-g.pct.mgh --annot seg rh aparc --sum /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/stats/rh.w-g.pct.stats --snr sysname Linux hostname roxy machine x86_64 user pkashyap UseRobust 0 Constructing seg from annotation Reading annotation /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.w-g.pct.mgh Vertex Area is 0.68087 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Tue Jul 23 10:05:18 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 892 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 995 voxels changed to hypointensity... 1946 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Tue Jul 23 10:06:03 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg mri_aparc2aseg --s seg --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 subject seg outvol /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading lh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial Loading lh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading rh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial Loading rh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.00 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 24 rescaling Left_Cerebellum_White_Matter from 86 --> 79 rescaling Left_Cerebellum_Cortex from 60 --> 45 rescaling Left_Thalamus from 94 --> 84 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 58 rescaling Left_Putamen from 80 --> 74 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 4 rescaling Fourth_Ventricle from 22 --> 2 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 51 rescaling CSF from 32 --> 5 rescaling Left_Accumbens_area from 62 --> 52 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 46 rescaling Right_Lateral_Ventricle from 13 --> 2 rescaling Right_Inf_Lat_Vent from 25 --> 20 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 46 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 58 rescaling Right_Putamen from 80 --> 70 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 57 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 5 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 581652 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 289 changed. pass 2: 29 changed. pass 3: 10 changed. pass 4: 1 changed. pass 5: 3 changed. pass 6: 1 changed. pass 7: 1 changed. pass 8: 1 changed. pass 9: 0 changed. nchanged = 0 Writing output aseg to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Tue Jul 23 10:15:36 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg mri_aparc2aseg --s seg --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 subject seg outvol /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading lh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial Loading lh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading rh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial Loading rh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.00 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 24 rescaling Left_Cerebellum_White_Matter from 86 --> 79 rescaling Left_Cerebellum_Cortex from 60 --> 45 rescaling Left_Thalamus from 94 --> 84 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 58 rescaling Left_Putamen from 80 --> 74 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 4 rescaling Fourth_Ventricle from 22 --> 2 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 51 rescaling CSF from 32 --> 5 rescaling Left_Accumbens_area from 62 --> 52 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 46 rescaling Right_Lateral_Ventricle from 13 --> 2 rescaling Right_Inf_Lat_Vent from 25 --> 20 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 46 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 58 rescaling Right_Putamen from 80 --> 70 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 57 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 5 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 581647 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 289 changed. pass 2: 29 changed. pass 3: 10 changed. pass 4: 1 changed. pass 5: 3 changed. pass 6: 1 changed. pass 7: 1 changed. pass 8: 1 changed. pass 9: 0 changed. nchanged = 0 Writing output aseg to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Tue Jul 23 10:25:45 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg mri_aparc2aseg --s seg --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 subject seg outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading lh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial Loading lh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading rh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial Loading rh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.00 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 24 rescaling Left_Cerebellum_White_Matter from 86 --> 79 rescaling Left_Cerebellum_Cortex from 60 --> 45 rescaling Left_Thalamus from 94 --> 84 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 58 rescaling Left_Putamen from 80 --> 74 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 4 rescaling Fourth_Ventricle from 22 --> 2 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 51 rescaling CSF from 32 --> 5 rescaling Left_Accumbens_area from 62 --> 52 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 46 rescaling Right_Lateral_Ventricle from 13 --> 2 rescaling Right_Inf_Lat_Vent from 25 --> 20 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 46 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 58 rescaling Right_Putamen from 80 --> 70 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 57 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 5 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 581647 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 289 changed. pass 2: 29 changed. pass 3: 10 changed. pass 4: 1 changed. pass 5: 3 changed. pass 6: 1 changed. pass 7: 1 changed. pass 8: 1 changed. pass 9: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Tue Jul 23 10:37:13 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Tue Jul 23 10:37:13 EDT 2019 setenv SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 cd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri /opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux roxy 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname roxy machine x86_64 user pkashyap input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Tue Jul 23 10:37:13 EDT 2019 Ended at Tue Jul 23 10:37:23 EDT 2019 Apas2aseg-Run-Time-Sec 10 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Tue Jul 23 10:37:23 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject seg $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject seg sysname Linux hostname roxy machine x86_64 user pkashyap UseRobust 0 atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) Computing euler number orig.nofix lheno = -14, rheno = -72 orig.nofix lhholes = 8, rhholes = 37 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Tue Jul 23 10:38:30 EDT 2019 /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg mri_aparc2aseg --s seg --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 subject seg outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aparc+aseg.mgz Reading lh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading lh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial Loading lh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading rh pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial Loading rh annotations from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/ribbon.mgz Loading filled from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8580 vertices from left hemi Ripped 8797 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aseg.mgz Loading Ctx Seg File /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1109007 Used brute-force search on 2410 voxels Fixing Parahip LH WM Found 10 clusters 0 k 1375.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 17.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 Fixing Parahip RH WM Found 11 clusters 0 k 1.000000 1 k 2.000000 2 k 2.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 5.000000 8 k 1682.000000 9 k 2.000000 10 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject seg --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject seg --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname roxy machine x86_64 user pkashyap UseRobust 0 atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0; ln -s /opt/freesurfer/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Tue Jul 23 10:48:29 EDT 2019 mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA1_exvivo.label --trgsubject seg --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 330 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4459 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA2_exvivo.label --trgsubject seg --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 580 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8489 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject seg --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4254 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject seg --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 371 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6354 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject seg --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 607 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6391 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject seg --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 297 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4367 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA6_exvivo.label --trgsubject seg --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 2307 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15896 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA44_exvivo.label --trgsubject seg --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 295 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4476 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA45_exvivo.label --trgsubject seg --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 490 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3912 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V1_exvivo.label --trgsubject seg --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 912 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5553 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V2_exvivo.label --trgsubject seg --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 2286 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10400 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.MT_exvivo.label --trgsubject seg --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 453 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2471 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject seg --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1349 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject seg --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1145 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 180 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2272 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1555 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2126 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 201 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2520 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1643 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 1125 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8160 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2000 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject seg --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 230 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1381 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject seg --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 598 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4003 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject seg --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 1042 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4376 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject seg --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 557 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject seg --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 483 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject seg --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 144528 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 465 mri_label2label: Done mris_label2annot --s seg --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label cmdline mris_label2annot --s seg --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname roxy machine x86_64 user pkashyap subject seg hemi lh SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 101488 unhit vertices Writing annot to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.BA_exvivo.annot mris_label2annot --s seg --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label cmdline mris_label2annot --s seg --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname roxy machine x86_64 user pkashyap subject seg hemi lh SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 119512 unhit vertices Writing annot to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab seg lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 296986 Total vertex volume 292823 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1196 717 2621 2.520 0.788 0.128 0.043 24 2.3 BA1_exvivo 4257 2858 7057 2.218 0.587 0.104 0.018 35 3.1 BA2_exvivo 1178 768 1190 1.882 0.449 0.122 0.023 8 1.1 BA3a_exvivo 2458 1636 3815 1.945 0.652 0.096 0.019 20 2.1 BA3b_exvivo 1768 1107 4106 3.046 0.586 0.101 0.019 14 1.3 BA4a_exvivo 1441 982 2524 2.633 0.335 0.089 0.014 7 0.9 BA4p_exvivo 11703 7794 27752 2.864 0.680 0.119 0.024 125 11.3 BA6_exvivo 2220 1521 5026 2.780 0.523 0.109 0.017 21 1.6 BA44_exvivo 2772 1925 6904 2.777 0.818 0.132 0.029 42 3.3 BA45_exvivo 2975 2110 4335 1.920 0.579 0.156 0.037 45 5.2 V1_exvivo 7723 5326 14080 2.257 0.649 0.150 0.031 119 10.0 V2_exvivo 2101 1452 4667 2.435 0.707 0.136 0.023 31 1.9 MT_exvivo 549 344 1801 3.552 0.787 0.113 0.022 6 0.4 perirhinal_exvivo 699 468 1538 2.850 0.821 0.080 0.019 4 0.5 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab seg lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 296986 Total vertex volume 292823 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 776 435 1417 2.316 0.656 0.144 0.052 21 2.0 BA1_exvivo 1736 1188 2604 2.051 0.438 0.098 0.016 13 1.1 BA2_exvivo 955 636 915 1.840 0.450 0.130 0.026 7 1.0 BA3a_exvivo 1514 1011 1823 1.663 0.422 0.066 0.008 5 0.5 BA3b_exvivo 1769 1112 4041 3.054 0.548 0.088 0.016 10 1.0 BA4a_exvivo 1172 796 2009 2.599 0.338 0.096 0.015 6 0.8 BA4p_exvivo 6515 4342 16410 2.939 0.716 0.123 0.025 73 6.6 BA6_exvivo 1385 948 3371 2.822 0.604 0.111 0.018 13 1.1 BA44_exvivo 1174 805 3384 2.950 0.838 0.135 0.033 19 1.6 BA45_exvivo 3159 2241 4686 1.934 0.579 0.150 0.036 45 5.3 V1_exvivo 3811 2690 6947 2.199 0.683 0.160 0.034 64 5.6 V2_exvivo 446 333 810 2.165 0.473 0.127 0.019 6 0.2 MT_exvivo 273 174 953 3.458 0.778 0.118 0.018 2 0.2 perirhinal_exvivo 331 217 812 3.161 0.649 0.048 0.008 1 0.1 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Tue Jul 23 10:58:45 EDT 2019 mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA1_exvivo.label --trgsubject seg --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 616 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4578 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA2_exvivo.label --trgsubject seg --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 770 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7457 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject seg --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 219 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4199 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject seg --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 550 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5072 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject seg --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6176 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject seg --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4683 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA6_exvivo.label --trgsubject seg --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 872 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13128 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA44_exvivo.label --trgsubject seg --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 669 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7581 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA45_exvivo.label --trgsubject seg --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 993 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6348 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V1_exvivo.label --trgsubject seg --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 982 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5709 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V2_exvivo.label --trgsubject seg --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 2524 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10540 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.MT_exvivo.label --trgsubject seg --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 935 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2867 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject seg --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1131 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject seg --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 803 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 229 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1105 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 252 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2940 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1765 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 253 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2436 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1459 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 454 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7413 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1113 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject seg --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1271 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject seg --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 559 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3791 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject seg --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 1224 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4661 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject seg --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 399 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject seg --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 767 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject seg --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = seg trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 FREESURFER_HOME /opt/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white Reading target registration /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 146765 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 309 mri_label2label: Done mris_label2annot --s seg --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label cmdline mris_label2annot --s seg --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname roxy machine x86_64 user pkashyap subject seg hemi rh SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 104910 unhit vertices Writing annot to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.BA_exvivo.annot mris_label2annot --s seg --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label cmdline mris_label2annot --s seg --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname roxy machine x86_64 user pkashyap subject seg hemi rh SUBJECTS_DIR /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0 ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 123992 unhit vertices Writing annot to /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab seg rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 297352 Total vertex volume 292288 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 1215 682 2374 2.455 0.735 0.141 0.061 28 3.0 BA1_exvivo 3656 2425 5956 2.247 0.592 0.120 0.026 46 4.3 BA2_exvivo 1209 827 1180 1.851 0.467 0.120 0.022 9 1.1 BA3a_exvivo 2363 1559 3130 1.759 0.506 0.098 0.021 19 2.1 BA3b_exvivo 1596 948 3320 2.944 0.380 0.088 0.022 12 1.3 BA4a_exvivo 1288 890 2372 2.664 0.420 0.087 0.013 6 0.6 BA4p_exvivo 7775 5138 19062 2.915 0.690 0.115 0.023 72 7.2 BA6_exvivo 3565 2426 7578 2.688 0.640 0.102 0.017 33 2.4 BA44_exvivo 4321 2982 9977 2.652 0.682 0.125 0.023 60 4.0 BA45_exvivo 3198 2279 5067 2.050 0.567 0.155 0.039 53 5.1 V1_exvivo 8031 5563 13810 2.215 0.638 0.156 0.037 133 13.2 V2_exvivo 2741 1891 5772 2.598 0.551 0.134 0.025 37 2.9 MT_exvivo 582 386 2333 3.782 0.738 0.091 0.019 5 0.4 perirhinal_exvivo 315 223 977 3.176 0.862 0.084 0.013 1 0.2 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab seg rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/mri/wm.mgz... reading input surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... reading input pial surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.pial... reading input white surface /tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0/seg/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 297352 Total vertex volume 292288 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1659569 mm^3 (det: 1.173862 ) lhCtxGM: 292973.106 292025.000 diff= 948.1 pctdiff= 0.324 rhCtxGM: 292359.335 291291.000 diff= 1068.3 pctdiff= 0.365 lhCtxWM: 263099.932 263523.500 diff= -423.6 pctdiff=-0.161 rhCtxWM: 265875.685 266021.500 diff= -145.8 pctdiff=-0.055 SubCortGMVol 60192.000 SupraTentVol 1206586.058 (1202744.000) diff=3842.058 pctdiff=0.318 SupraTentVolNotVent 1176975.058 (1173133.000) diff=3842.058 pctdiff=0.326 BrainSegVol 1368970.000 (1364554.000) diff=4416.000 pctdiff=0.323 BrainSegVolNotVent 1333823.000 (1335125.058) diff=-1302.058 pctdiff=-0.098 BrainSegVolNotVent 1333823.000 CerebellumVol 160545.000 VentChorVol 29611.000 3rd4th5thCSF 5536.000 CSFVol 1120.000, OptChiasmVol 145.000 MaskVol 1686396.000 874 452 1576 2.444 0.705 0.127 0.053 17 1.6 BA1_exvivo 2061 1369 3668 2.359 0.582 0.121 0.034 30 3.0 BA2_exvivo 1064 717 958 1.860 0.433 0.121 0.023 8 0.9 BA3a_exvivo 1810 1244 2087 1.600 0.372 0.084 0.013 9 1.0 BA3b_exvivo 916 530 2021 3.024 0.431 0.110 0.033 9 1.1 BA4a_exvivo 1051 749 1986 2.711 0.449 0.087 0.013 5 0.6 BA4p_exvivo 5068 3304 12905 2.966 0.720 0.115 0.024 45 4.9 BA6_exvivo 886 589 2013 2.847 0.616 0.105 0.021 9 0.7 BA44_exvivo 881 621 2516 3.004 0.759 0.129 0.026 12 0.9 BA45_exvivo 2992 2140 4738 2.059 0.569 0.149 0.036 45 4.4 V1_exvivo 4190 2943 6690 2.089 0.613 0.171 0.044 83 8.1 V2_exvivo 384 255 711 2.572 0.249 0.119 0.023 4 0.3 MT_exvivo 361 231 1446 3.712 0.753 0.076 0.017 3 0.2 perirhinal_exvivo 235 153 852 3.686 0.769 0.088 0.013 1 0.1 entorhinal_exvivo Started at Mon Jul 22 11:54:25 EDT 2019 Ended at Tue Jul 23 11:08:20 EDT 2019 #@#%# recon-all-run-time-hours 23.232 recon-all -s seg finished without error at Tue Jul 23 11:08:21 EDT 2019 donehostnameroxycmdlinerecon-all -all -i /home/pkashyap/data/subj01/anat/t11_sanlm.nii.gz -openmp 64 -subjid seg -sd .versionNoneenviron{'FSLDIR': '/usr/share/fsl/5.0', 'MODULE_VERSION': '3.2.10', 'POSSUMDIR': '/usr/share/fsl/5.0', 'BASH_FUNC_module%%': '() { eval `/usr/bin/modulecmd bash $*`\n}', 'MINC_BIN_DIR': '/opt/freesurfer/6.0/mni/bin', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'FIX_VERTEX_AREA': '', 'SSH_CLIENT': '10.76.253.211 42756 22', 'FSLREMOTECALL': '', 'USER': 'pkashyap', 'FSL_BIN': '/usr/share/fsl/5.0/bin', 'HOME': '/home/pkashyap', 'PATH': 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'OS': 'Linux', 'FSLCONVERT': '/usr/bin/convert', 'FS_OVERRIDE': '0'}platformLinux-4.4.0-154-generic-x86_64-with-debian-stretch-sidstartTime2019-07-22T15:54:25.729915duration83635.490682dependencies not a dynamic executablecommand_path/opt/freesurfer/bin/recon-allendTime2019-07-23T15:08:21.220597cwd/tmp/tmp4CZWe1/MyWorkflow/_sess_id_1_subj_id_01/recon/mapflow/_recon0merged