Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /prod2/allegra/barcslong_t1/SUBJECTS Actual FREESURFER_HOME /opt/freesurfer-5.1.0 -rw-rw-r-- 1 Skhadka2 users 184952 Feb 1 19:19 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts/recon-all.log Linux hhlxnrcas26 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Mon Feb 4 14:12:39 EST 2013 mri_convert -at /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta -odt uchar /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1/mri/orig/001.mgz /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/orig.mgz mri_convert -at /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta -odt uchar /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1/mri/orig/001.mgz /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999998, 0, -0.00174533) j_ras = (0, 1, 0) k_ras = (-0.00174533, 0, 0.999998) INFO: Applying transformation from file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.009 -0.006 -2.394; 0.009 1.000 -0.019 -3.124; 0.007 0.019 1.000 -0.793; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/orig.mgz... mri_add_xform_to_header -c /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/talairach.xfm /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/orig.mgz /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Feb 4 14:12:57 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cp /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/talairach.xfm /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Feb 4 14:12:57 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5686, pval=0.2115 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Mon Feb 4 14:12:57 EST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/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 1.18 2011/03/02 20:16:39 nicks Exp $ Linux hhlxnrcas26 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux Mon Feb 4 14:12:57 EST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.18683 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18683/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18683/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve 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 = (1.16415e-10, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.18683/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Feb 4 14:13:04 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.18683/nu0.mnc ./tmp.mri_nu_correct.mni.18683/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18683/0/ [Skhadka2@hhlxnrcas26:/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/] [2013-02-04 14:13:04] running: /opt/freesurfer-5.0.0/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18683/0/ ./tmp.mri_nu_correct.mni.18683/nu0.mnc ./tmp.mri_nu_correct.mni.18683/nu1.imp 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: 11 CV of field change: 0.000972427 [Skhadka2@hhlxnrcas26:/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/] [2013-02-04 14:13:21] running: /opt/freesurfer-5.0.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.18683/nu0.mnc ./tmp.mri_nu_correct.mni.18683/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Feb 4 14:13:30 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.18683/nu1.mnc ./tmp.mri_nu_correct.mni.18683/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.18683/1/ [Skhadka2@hhlxnrcas26:/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/] [2013-02-04 14:13:30] running: /opt/freesurfer-5.0.0/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18683/1/ ./tmp.mri_nu_correct.mni.18683/nu1.mnc ./tmp.mri_nu_correct.mni.18683/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 7 CV of field change: 0.00093793 [Skhadka2@hhlxnrcas26:/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/] [2013-02-04 14:13:41] running: /opt/freesurfer-5.0.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.18683/nu1.mnc ./tmp.mri_nu_correct.mni.18683/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.18683/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18683/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.18683/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18683/ones.mgz sysname Linux hostname hhlxnrcas26 machine x86_64 user Skhadka2 input ./tmp.mri_nu_correct.mni.18683/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.18683/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18683/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18683/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18683/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18683/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18683/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18683/input.mean.dat sysname Linux hostname hhlxnrcas26 machine x86_64 user Skhadka2 Loading ./tmp.mri_nu_correct.mni.18683/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.18683/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18683/ones.mgz --i ./tmp.mri_nu_correct.mni.18683/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18683/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18683/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18683/ones.mgz --i ./tmp.mri_nu_correct.mni.18683/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18683/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18683/output.mean.dat sysname Linux hostname hhlxnrcas26 machine x86_64 user Skhadka2 Loading ./tmp.mri_nu_correct.mni.18683/ones.mgz Loading ./tmp.mri_nu_correct.mni.18683/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.18683/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.18683/nu2.mnc ./tmp.mri_nu_correct.mni.18683/nu2.mnc mul .97715845172386560078 Saving result to './tmp.mri_nu_correct.mni.18683/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.18683/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.18683/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.18683/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (1.16415e-10, 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 14 seconds. mapping (15, 151) to ( 3, 110) Mon Feb 4 14:15:10 EST 2013 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Mon Feb 4 14:15:10 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.068 0.048 -0.041 -2.786; -0.053 0.940 0.377 -6.850; 0.047 -0.380 0.996 -3.954; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 3 minutes and 12 seconds. MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 white matter peak found at 111 white matter peak found at 109 gm peak at 69 (69), valley at 30 (30) csf peak at 35, setting threshold to 57 white matter peak found at 111 white matter peak found at 110 gm peak at 72 (72), valley at 52 (52) csf peak at 36, setting threshold to 60 #-------------------------------------------- #@# Skull Stripping Mon Feb 4 14:18:24 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/brainmask.mgz ./brainmask_S1326RML.mgz `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/brainmask.mgz' -> `./brainmask_S1326RML.mgz' mri_mask -keep_mask_deletion_edits T1.mgz brainmask_S1326RML.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_S1326RML.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #------------------------------------- #@# EM Registration Mon Feb 4 14:18:33 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/talairach.lta transforms/talairach.lta `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/talairach.lta' -> `transforms/talairach.lta' #-------------------------------------- #@# CA Normalize Mon Feb 4 14:18:33 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/aseg.mgz aseg_S1326RML.mgz `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/aseg.mgz' -> `aseg_S1326RML.mgz' mri_ca_normalize -long aseg_S1326RML.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using longitudinal segmentation volume aseg_S1326RML.mgz to generate control points... using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 104 resetting gm mean[0]: 63 --> 63 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (59, 57, 53) --> (195, 212, 217) using (104, 109, 135) as brain centroid... mean wm in atlas = 104, using box (87,90,115) --> (120, 128,155) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 0.945 scaling channel 0 by 0.945455 using 244171 sample points... INFO: compute sample coordinates transform 1.088 -0.028 -0.089 3.994; 0.061 1.049 0.380 -69.740; 0.085 -0.368 0.951 21.101; 0.000 0.000 0.000 1.000; INFO: transform used using 120024 total control points for intensity normalization... bias field = 0.984 +- 0.072 106 of 120024 control points discarded using 120024 total control points for intensity normalization... bias field = 1.028 +- 0.051 144 of 120024 control points discarded using 120024 total control points for intensity normalization... bias field = 1.023 +- 0.042 184 of 120024 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 2 minutes and 38 seconds. #-------------------------------------- #@# CA Reg Mon Feb 4 14:21:12 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri mri_ca_register -nobigventricles -levels 2 -A 1 -l /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/talairach.m3z and applying inverse registration identity.nofile renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 zcat /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/talairach.m3z label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25918.771 ms 0001: dt=0.000000, rms=0.373 (0.182%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24443.275 ms 0002: dt=0.000000, rms=0.373 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.373, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25306.754 ms 0003: dt=0.000000, rms=0.373 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.373, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24934.357 ms 0004: dt=0.000000, rms=0.373 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.373, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25028.158 ms 0005: dt=0.000000, rms=0.373 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.19904 (17) Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (6353 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (6353 voxels, peak = 14), gca=14.4 gca peak = 0.14022 (22) mri peak = 0.22463 (17) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (6675 voxels, overlap=0.013) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (6675 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.27231 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (437 voxels, overlap=0.994) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (437 voxels, peak = 100), gca=100.0 gca peak = 0.19192 (97) mri peak = 0.18480 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (487 voxels, overlap=0.988) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (487 voxels, peak = 97), gca=97.0 gca peak = 0.24007 (63) mri peak = 0.13343 (63) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1344 voxels, overlap=0.994) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1344 voxels, peak = 63), gca=63.0 gca peak = 0.29892 (64) mri peak = 0.19350 (65) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1441 voxels, overlap=0.988) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1441 voxels, peak = 64), gca=64.0 gca peak = 0.12541 (104) mri peak = 0.13262 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47077 voxels, overlap=0.774) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47077 voxels, peak = 104), gca=104.0 gca peak = 0.13686 (104) mri peak = 0.13434 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55958 voxels, overlap=0.813) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55958 voxels, peak = 104), gca=104.0 gca peak = 0.11691 (63) mri peak = 0.04335 (60) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (68532 voxels, overlap=0.945) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (68532 voxels, peak = 60), gca=59.8 gca peak = 0.13270 (63) mri peak = 0.04148 (63) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (69793 voxels, overlap=0.986) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (69793 voxels, peak = 60), gca=59.8 gca peak = 0.15182 (70) mri peak = 0.12616 (71) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1395 voxels, overlap=0.929) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1395 voxels, peak = 70), gca=70.0 gca peak = 0.14251 (76) mri peak = 0.14826 (71) Left_Caudate (11): linear fit = 0.93 x + 0.0 (1353 voxels, overlap=0.512) Left_Caudate (11): linear fit = 0.93 x + 0.0 (1353 voxels, peak = 70), gca=70.3 gca peak = 0.12116 (60) mri peak = 0.05745 (63) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36947 voxels, overlap=0.984) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36947 voxels, peak = 60), gca=60.0 gca peak = 0.12723 (61) mri peak = 0.05497 (59) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (39291 voxels, overlap=0.974) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (39291 voxels, peak = 58), gca=58.0 gca peak = 0.22684 (88) mri peak = 0.19939 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6276 voxels, overlap=0.687) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6276 voxels, peak = 90), gca=90.2 gca peak = 0.21067 (87) mri peak = 0.16865 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7254 voxels, overlap=0.730) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7254 voxels, peak = 89), gca=89.2 gca peak = 0.25455 (62) mri peak = 0.31727 (66) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (498 voxels, overlap=0.864) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (498 voxels, peak = 65), gca=65.1 gca peak = 0.39668 (62) mri peak = 0.31627 (66) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (653 voxels, overlap=0.400) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (653 voxels, peak = 65), gca=65.1 gca peak = 0.10129 (93) mri peak = 0.11130 (86) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4295 voxels, overlap=0.755) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4295 voxels, peak = 88), gca=88.3 gca peak = 0.12071 (89) mri peak = 0.14335 (86) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4277 voxels, overlap=0.882) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4277 voxels, peak = 85), gca=84.5 gca peak = 0.13716 (82) mri peak = 0.10726 (86) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3235 voxels, overlap=0.991) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3235 voxels, peak = 82), gca=82.0 gca peak = 0.15214 (84) mri peak = 0.10055 (86) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3093 voxels, overlap=0.918) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3093 voxels, peak = 84), gca=84.0 gca peak = 0.08983 (85) mri peak = 0.11458 (91) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13160 voxels, overlap=0.741) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13160 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.11278 (96) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1704 voxels, overlap=0.613) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1704 voxels, peak = 94), gca=94.3 gca peak = 0.12914 (94) mri peak = 0.14841 (95) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1715 voxels, overlap=0.757) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1715 voxels, peak = 94), gca=94.0 gca peak = 0.21100 (36) mri peak = 0.20000 (23) Third_Ventricle (14): linear fit = 0.60 x + 0.0 (130 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.60 x + 0.0 (130 voxels, peak = 22), gca=21.6 gca peak = 0.13542 (27) mri peak = 0.24940 (17) Fourth_Ventricle (15): linear fit = 0.55 x + 0.0 (1248 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.55 x + 0.0 (1248 voxels, peak = 15), gca=14.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.64 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25180.791 ms 0006: dt=0.000000, rms=0.369 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22318.678 ms 0007: dt=0.000000, rms=0.369 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22337.924 ms 0008: dt=0.000000, rms=0.369 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22129.791 ms 0009: dt=0.000000, rms=0.369 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22137.016 ms 0010: dt=0.000000, rms=0.369 (0.000%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59810.367 ms iter 0, gcam->neg = 26 after 200 iterations, nbhd size=2, neg = 9 starting rms=0.006, neg=9, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28721.641 ms iter 1, dt=0.000000: new neg 9, old_neg 9, delta 0, rms=0.006 (-0.001%) ---------- unfolding failed - restoring original position -------------------- 0011: dt=3.166667, rms=0.369 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64659.797 ms iter 0, gcam->neg = 43 after 200 iterations, nbhd size=4, neg = 9 starting rms=0.007, neg=9, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29847.270 ms iter 1, dt=0.000000: new neg 9, old_neg 9, delta 0, rms=0.007 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0012: dt=4.800000, rms=0.369 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62453.984 ms iter 0, gcam->neg = 8 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30125.898 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0013: dt=0.216000, rms=0.369 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61559.570 ms iter 0, gcam->neg = 9 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.001, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29855.904 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0014: dt=0.252000, rms=0.369 (0.000%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.368, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60695.363 ms iter 0, gcam->neg = 30 after 200 iterations, nbhd size=1, neg = 10 starting rms=0.006, neg=10, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30392.047 ms iter 1, dt=0.000000: new neg 10, old_neg 10, delta 0, rms=0.006 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0015: dt=3.545455, rms=0.369 (-0.231%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59328.258 ms iter 0, gcam->neg = 83 after 200 iterations, nbhd size=2, neg = 16 starting rms=0.011, neg=16, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 38788.961 ms iter 1, dt=0.000000: new neg 16, old_neg 16, delta 0, rms=0.011 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0016: dt=8.000000, rms=0.369 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73437.812 ms iter 0, gcam->neg = 49 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.004, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 35994.117 ms iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.004 (0.008%) ---------- unfolding failed - restoring original position -------------------- 0017: dt=0.720000, rms=0.369 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.369, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 72289.719 ms iter 0, gcam->neg = 9 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.001, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 36043.652 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0018: dt=0.252000, rms=0.369 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 1 hours, 15 minutes and 42 seconds. #-------------------------------------- #@# CA Reg Inv Mon Feb 4 15:36:54 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Mon Feb 4 15:38:45 EST 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 10879547 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 2 minutes and 0 seconds. #-------------------------------------- #@# SkullLTA Mon Feb 4 15:40:45 EST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=15.0 skull bounding box = (48, 47, 40) --> (206, 211, 243) using (101, 102, 142) as brain centroid... mean wm in atlas = 126, using box (82,82,117) --> (120, 122,167) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10282.8, old_max_log_p =-10364.9 (thresh=-10354.5) 1.007 -0.026 -0.083 13.127; 0.056 1.144 0.303 -71.453; 0.087 -0.164 0.922 -1.706; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10282.5, old_max_log_p =-10282.8 (thresh=-10272.5) 1.007 -0.026 -0.083 13.127; 0.052 1.059 0.280 -57.011; 0.087 -0.164 0.922 -1.706; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10271.7, old_max_log_p =-10282.5 (thresh=-10272.2) 1.065 0.008 -0.082 1.479; 0.024 1.093 0.322 -63.316; 0.077 -0.194 0.879 8.944; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10271.7, old_max_log_p =-10271.7 (thresh=-10261.4) 1.065 0.008 -0.082 1.479; 0.024 1.093 0.322 -63.316; 0.077 -0.194 0.879 8.944; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10269.5, old_max_log_p =-10271.7 (thresh=-10261.4) 1.062 0.008 -0.082 1.770; 0.024 1.097 0.323 -63.965; 0.077 -0.193 0.878 9.058; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06207 0.00765 -0.08170 1.76984; 0.02414 1.09674 0.32321 -63.96534; 0.07706 -0.19340 0.87755 9.05781; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.06207 0.00765 -0.08170 1.76984; 0.02414 1.09674 0.32321 -63.96534; 0.07706 -0.19340 0.87755 9.05781; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10269.5 tol 0.000010 Resulting transform: 1.062 0.008 -0.082 1.770; 0.024 1.097 0.323 -63.965; 0.077 -0.193 0.878 9.058; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10269.5 (old=-10364.9) transform before final EM align: 1.062 0.008 -0.082 1.770; 0.024 1.097 0.323 -63.965; 0.077 -0.193 0.878 9.058; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06207 0.00765 -0.08170 1.76984; 0.02414 1.09674 0.32321 -63.96534; 0.07706 -0.19340 0.87755 9.05781; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.06207 0.00765 -0.08170 1.76984; 0.02414 1.09674 0.32321 -63.96534; 0.07706 -0.19340 0.87755 9.05781; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 1144481.5 tol 0.000000 final transform: 1.062 0.008 -0.082 1.770; 0.024 1.097 0.323 -63.965; 0.077 -0.193 0.878 9.058; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 31 minutes and 57 seconds. #-------------------------------------- #@# SubCort Seg Mon Feb 4 16:12:43 EST 2013 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname hhlxnrcas26 machine x86_64 user Skhadka2 Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/S1326RML1_to_S1326RML1.long.S1326RML.lta `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/S1326RML1_to_S1326RML1.long.S1326RML.lta' cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML3_to_S1326RML.lta /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/S1326RML3_to_S1326RML1.long.S1326RML.lta `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML3_to_S1326RML.lta' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/S1326RML3_to_S1326RML1.long.S1326RML.lta' mri_fuse_segmentations -a aseg.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz S1326RML1.long.S1326RML S1326RML1 S1326RML3 aseg.fused.mgz fusing took 0 minutes and 34 seconds. using aseg.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/norm.mgz and processing 2 timepoints, writing to aseg.fused.mgz loading data for subject S1326RML1 ... loading data for subject S1326RML3 ... fusing... relabeled 6846 CC labels writing fused segmentation to aseg.fused.mgz mri_ca_label -align -nobigventricles -r /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.fused.mgz -ri /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/aseg.auto_noCCseg.label_intensities.txt norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading previously labeled volume from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.fused.mgz... reading intensity scaling from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/aseg.auto_noCCseg.label_intensities.txt... reading 1 input volumes... reading classifier array from /opt/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2008-03-26.gca reading label scales and offsets from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/aseg.auto_noCCseg.label_intensities.txt reading intensity scales from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/aseg.auto_noCCseg.label_intensities.txt label Left_Cerebral_Exterior (1): 0.66 + 0.0 label Left_Cerebral_White_Matter (2): 1.02 + 0.0 label Left_Cerebral_Cortex (3): 0.97 + 0.0 label Left_Lateral_Ventricle (4): 0.66 + 0.0 label Left_Inf_Lat_Vent (5): 1.00 + 0.0 label Left_Cerebellum_White_Matter (7): 1.02 + 0.0 label Left_Cerebellum_Cortex (8): 1.00 + 0.0 label Left_Thalamus (9): 1.02 + 0.0 label Left_Thalamus_Proper (10): 1.02 + 0.0 label Left_Caudate (11): 0.98 + 0.0 label Left_Putamen (12): 1.05 + 0.0 label Left_Pallidum (13): 1.05 + 0.0 label Third_Ventricle (14): 0.59 + 0.0 label Fourth_Ventricle (15): 0.61 + 0.0 label Brain_Stem (16): 1.05 + 0.0 label Left_Hippocampus (17): 1.00 + 0.0 label Left_Amygdala (18): 1.10 + 0.0 label CSF (24): 0.66 + 0.0 label Left_Accumbens_area (26): 0.98 + 0.0 label Left_VentralDC (28): 1.05 + 0.0 label Right_Cerebral_Exterior (40): 0.66 + 0.0 label Right_Cerebral_White_Matter (41): 1.02 + 0.0 label Right_Cerebral_Cortex (42): 0.97 + 0.0 label Right_Lateral_Ventricle (43): 0.78 + 0.0 label Right_Inf_Lat_Vent (44): 1.00 + 0.0 label Right_Cerebellum_White_Matter (46): 1.02 + 0.0 label Right_Cerebellum_Cortex (47): 0.97 + 0.0 label Right_Thalamus (48): 1.02 + 0.0 label Right_Thalamus_Proper (49): 1.05 + 0.0 label Right_Caudate (50): 1.05 + 0.0 label Right_Putamen (51): 1.05 + 0.0 label Right_Pallidum (52): 1.07 + 0.0 label Right_Hippocampus (53): 1.00 + 0.0 label Right_Amygdala (54): 1.08 + 0.0 label Right_Accumbens_area (58): 1.05 + 0.0 label Right_VentralDC (60): 1.08 + 0.0 label Fifth_Ventricle (72): 0.66 + 0.0 label Left_Lateral_Ventricles (75): 0.66 + 0.0 label Right_Lateral_Ventricles (76): 0.66 + 0.0 label WM_hypointensities (77): 1.02 + 0.0 label Left_WM_hypointensities (78): 1.02 + 0.0 label Right_WM_hypointensities (79): 1.02 + 0.0 label non_WM_hypointensities (80): 1.02 + 0.0 label Left_non_WM_hypointensities (81): 1.02 + 0.0 label Right_non_WM_hypointensities (82): 1.02 + 0.0 label (186): 0.00 + 0.0 label (187): 0.00 + 0.0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized pass 1: 82712 changed. image ll: -2.269, PF=1.000 pass 2: 30761 changed. image ll: -2.264, PF=1.000 pass 3: 10338 changed. pass 4: 4284 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 6 minutes and 53 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/cc_up.lta S1326RML1.long.S1326RML will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/transforms/cc_up.lta reading aseg from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.auto_noCCseg.mgz reading norm from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/norm.mgz 55813 voxels in left wm, 185175 in right wm, xrange [108, 133] searching rotation angles z=[-7 7], y=[-10 4] searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 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 global minimum found at slice 126.0, rotations (-3.22, 0.89) final transformation (x=126.0, yr=-3.218, zr=0.891): 0.998 -0.016 -0.056 11.058; 0.016 1.000 -0.001 12.169; 0.056 -0.000 0.998 -4.874; 0.000 0.000 0.000 1.000; updating x range to be [125, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 149 113 eigenvectors: 0.000 -0.000 1.000; -0.234 -0.972 0.000; 0.972 -0.234 -0.000; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.auto.mgz... corpus callosum matter segmentation took 4.1 minutes #-------------------------------------- #@# Merge ASeg Mon Feb 4 16:24:27 EST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Feb 4 16:24:27 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 1536 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 5 minutes and 18 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 109 gm peak at 70 (70), valley at 57 (57) csf peak at 18, setting threshold to 52 white matter peak found at 111 white matter peak found at 110 gm peak at 72 (72), valley at 42 (42) csf peak at 19, setting threshold to 54 #-------------------------------------------- #@# Mask BFS Mon Feb 4 16:29:50 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1913366 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Feb 4 16:29:55 EST 2013 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname hhlxnrcas26 machine x86_64 user Skhadka2 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname hhlxnrcas26 machine x86_64 user Skhadka2 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (102.0): 101.8 +- 7.4 [80.0 --> 125.0] GM (74.0) : 71.0 +- 11.0 [30.0 --> 96.0] setting bottom of white matter range to 82.0 setting top of gray matter range to 93.0 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... 3812 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2960 filled 5472 bright non-wm voxels segmented. 1520 diagonally connected voxels added... white matter segmentation took 2.7 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.95 minutes reading wm segmentation from wm.seg.mgz... 299 voxels added to wm to prevent paths from MTL structures to cortex 1501 additional wm voxels added 0 additional wm voxels added SEG EDIT: 66197 voxels turned on, 45067 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 99 new 99 115,126,128 old 99 new 99 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 17 found - 17 modified | TOTAL: 23 pass 2 (xy-): 0 found - 17 modified | TOTAL: 23 pass 1 (yz+): 18 found - 18 modified | TOTAL: 41 pass 2 (yz+): 0 found - 18 modified | TOTAL: 41 pass 1 (yz-): 11 found - 11 modified | TOTAL: 52 pass 2 (yz-): 0 found - 11 modified | TOTAL: 52 pass 1 (xz+): 12 found - 12 modified | TOTAL: 64 pass 2 (xz+): 0 found - 12 modified | TOTAL: 64 pass 1 (xz-): 12 found - 12 modified | TOTAL: 76 pass 2 (xz-): 0 found - 12 modified | TOTAL: 76 Iteration Number : 1 pass 1 (+++): 24 found - 24 modified | TOTAL: 24 pass 2 (+++): 0 found - 24 modified | TOTAL: 24 pass 1 (+++): 12 found - 12 modified | TOTAL: 36 pass 2 (+++): 0 found - 12 modified | TOTAL: 36 pass 1 (+++): 6 found - 6 modified | TOTAL: 42 pass 2 (+++): 0 found - 6 modified | TOTAL: 42 pass 1 (+++): 4 found - 4 modified | TOTAL: 46 pass 2 (+++): 0 found - 4 modified | TOTAL: 46 Iteration Number : 1 pass 1 (++): 39 found - 39 modified | TOTAL: 39 pass 2 (++): 0 found - 39 modified | TOTAL: 39 pass 1 (+-): 23 found - 23 modified | TOTAL: 62 pass 2 (+-): 0 found - 23 modified | TOTAL: 62 pass 1 (--): 27 found - 27 modified | TOTAL: 89 pass 2 (--): 0 found - 27 modified | TOTAL: 89 pass 1 (-+): 19 found - 19 modified | TOTAL: 108 pass 2 (-+): 0 found - 19 modified | TOTAL: 108 Iteration Number : 2 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 0 found - 0 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 0 found - 0 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 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 = 241 (out of 627395: 0.038413) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done mri_mask -transfer 255 -keep_mask_deletion_edits -xform /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta wm.mgz /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1/mri/wm.mgz wm.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol transform file name is /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/mri/transforms/S1326RML1_to_S1326RML.lta DoAbs = 0 Apply the given LTA xfrom to the mask volume Reading transform ... Found 16777216 voxels in mask Writing masked volume to wm.mgz...done. #-------------------------------------------- #@# Fill Mon Feb 4 16:34:10 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.088 -0.028 -0.089 3.994; 0.061 1.049 0.380 -69.740; 0.085 -0.368 0.951 21.101; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.088 -0.028 -0.089 3.994; 0.061 1.049 0.380 -69.740; 0.085 -0.368 0.951 21.101; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1586 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) need search nearby using seed (125, 121, 152), TAL = (3.0, 24.0, 7.0) talairach voxel to voxel transform 0.911 0.048 0.067 -1.730; -0.021 0.835 -0.335 65.377; -0.090 0.319 0.916 3.269; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 121, 152) --> (3.0, 24.0, 7.0) done. writing output to filled.mgz... filling took 1.3 minutes talairach cc position changed to (3.00, 24.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 24.00, 7.00) SRC: (111.62, 113.22, 171.52) search lh wm seed point around talairach space (-15.00, 24.00, 7.00), SRC: (144.41, 112.48, 168.29) 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 ... #-------------------------------------------- #@# Make White Surf lh Mon Feb 4 16:35:31 EST 2013 cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.white /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.white' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig' cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.white /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig_white `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.white' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig_white' cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.pial /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig_pial `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.pial' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig_pial' /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_make_surfaces -orig_white orig_white -orig orig_white -long -max 3.5 -noaparc -whiteonly -mgz -T1 brain.finalsurfs S1326RML1.long.S1326RML lh reading original vertex positions from orig_white only generating white matter surface using orig_white starting white location... Using longitudinal scheme using max_thickness = 3.5 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 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/filled.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/brain.finalsurfs.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/wm.mgz... 6570 bright wm thresholded. 6215 bright non-wm voxels segmented. reading original surface position from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig_white... computing class statistics... border white: 252030 voxels (1.50%) border gray 280397 voxels (1.67%) WM (95.0): 95.6 +- 6.8 [70.0 --> 110.0] GM (84.0) : 82.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.1 (was 70) setting MAX_BORDER_WHITE to 109.8 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 51.2 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.91 +- 0.25 (0.05-->6.65) (max @ vno 59248 --> 59267) face area 0.34 +- 0.16 (0.00-->5.90) mean absolute distance = 0.50 +- 0.74 2422 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=73 using class modes intead of means.... mean inside = 93.1, mean outside = 78.6 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.9, 186 (185) missing vertices, mean dist 0.2 [0.5 (%28.3)->0.5 (%71.7))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.10-->6.78) (max @ vno 104050 --> 97683) face area 0.34 +- 0.16 (0.00-->7.65) mean absolute distance = 0.32 +- 0.56 2716 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4118623.8, rms=5.89 001: dt: 0.5000, sse=3696713.2, rms=3.80 002: dt: 0.5000, sse=4056385.8, rms=2.87 003: dt: 0.5000, sse=4358733.0, rms=2.51 004: dt: 0.5000, sse=4590776.5, rms=2.38 rms = 2.36, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=4720488.5, rms=2.36 006: dt: 0.2500, sse=3071829.5, rms=1.60 007: dt: 0.2500, sse=2904023.2, rms=1.46 rms = 1.44, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=2835192.2, rms=1.44 rms = 1.42, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=2802372.0, rms=1.42 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.0, 169 (88) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.2 (%31.2))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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 0.92 +- 0.25 (0.08-->6.84) (max @ vno 58235 --> 59267) face area 0.36 +- 0.18 (0.00-->9.02) mean absolute distance = 0.27 +- 0.46 3392 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3056673.2, rms=3.34 010: dt: 0.5000, sse=3315191.2, rms=2.01 011: dt: 0.5000, sse=3572583.5, rms=1.85 rms = 1.81, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=3781446.8, rms=1.81 013: dt: 0.2500, sse=3156945.5, rms=1.30 014: dt: 0.2500, sse=3041642.2, rms=1.22 rms = 1.22, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=2996174.5, rms=1.22 rms = 1.20, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=2970752.5, rms=1.20 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.7, 160 (67) missing vertices, mean dist -0.1 [0.3 (%66.5)->0.2 (%33.5))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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 (0.09-->7.02) (max @ vno 58235 --> 59267) face area 0.35 +- 0.17 (0.00-->9.26) mean absolute distance = 0.24 +- 0.37 3267 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3084505.2, rms=2.61 017: dt: 0.5000, sse=3350148.0, rms=1.80 018: dt: 0.5000, sse=3480388.5, rms=1.73 rms = 1.73, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3221358.5, rms=1.36 020: dt: 0.2500, sse=3130781.0, rms=1.17 rms = 1.15, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3105870.2, rms=1.15 rms = 1.13, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3085892.8, rms=1.13 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.4, 178 (65) missing vertices, mean dist -0.1 [0.3 (%54.8)->0.2 (%45.2))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3099244.2, rms=1.53 023: dt: 0.5000, sse=3725575.0, rms=1.24 rms = 1.42, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3457651.8, rms=1.04 025: dt: 0.2500, sse=3337179.5, rms=0.98 rms = 0.96, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3361263.2, rms=0.96 rms = 0.94, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3363836.5, rms=0.94 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 9 non-cortical segments detected only using segment with 1872 vertices erasing segment 1 (vno[0] = 75765) erasing segment 2 (vno[0] = 82547) erasing segment 3 (vno[0] = 86381) erasing segment 4 (vno[0] = 94211) erasing segment 5 (vno[0] = 95870) erasing segment 6 (vno[0] = 98535) erasing segment 7 (vno[0] = 98624) erasing segment 8 (vno[0] = 105841) writing cortex label to /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/label/lh.cortex.label... LabelWrite: saving to /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/label/lh.cortex.label writing curvature file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.curv writing smoothed area to lh.area writing curvature file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.area vertex spacing 0.91 +- 0.26 (0.07-->7.14) (max @ vno 58235 --> 59267) face area 0.35 +- 0.17 (0.00-->9.44) refinement took 7.3 minutes #-------------------------------------------- #@# Smooth2 lh Mon Feb 4 16:42:53 EST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts 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 Mon Feb 4 16:42:59 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.4 mm, total surface area = 82170 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.106 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 0.9 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 293 vertices thresholded to be in k1 ~ [-0.23 0.28], k2 ~ [-0.08 0.05] total integrated curvature = 0.564*4pi (7.081) --> 0 handles ICI = 1.5, FI = 9.3, variation=157.608 148 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 134 vertices thresholded to be in [-0.14 0.14] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Mon Feb 4 16:45:59 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm S1326RML1.long.S1326RML 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 [ S1326RML1.long.S1326RML/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 [ 223 ] Gb_filter = 0 WARN: S lookup min: -0.210981 WARN: S explicit min: 0.000000 vertex = 1100 #-------------------------------------------- #@# Sphere lh Mon Feb 4 16:46:07 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts cp /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.sphere /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.sphere #-------------------------------------------- #@# Surf Reg lh Mon Feb 4 16:46:08 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_register -curv -nosulc -norot /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.sphere.reg /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif... will not use the sulcal depth map will not rigidly align the surface writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.023, std = 0.249 curvature mean = 0.003, std = 0.065 curvature mean = 0.026, std = 0.429 curvature mean = 0.003, std = 0.079 curvature mean = 0.022, std = 0.611 curvature mean = 0.003, std = 0.086 curvature mean = 0.014, std = 0.741 curvature mean = 0.004, std = 0.089 curvature mean = 0.005, std = 0.840 #-------------------------------------------- #@# Jacobian white lh Mon Feb 4 17:01:53 EST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Mon Feb 4 17:01:56 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mrisp_paint -a 5 /opt/freesurfer/average/lh.average.curvature.filled.buckner40.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.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Feb 4 17:01:59 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/label/lh.aparc.annot S1326RML1.long.S1326RML lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline will refine the initial labeling read-in from -R reading precomputed parcellation from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/label/lh.aparc.annot... $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) 000: 1151 changed, 129478 examined... 001: 280 changed, 5771 examined... 002: 99 changed, 1677 examined... 003: 31 changed, 637 examined... 004: 14 changed, 203 examined... 005: 3 changed, 92 examined... 006: 0 changed, 21 examined... 000: 65 total segments, 10 labels (15 vertices) changed 001: 55 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 309 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 11 seconds. #-------------------------------------------- #@# Make Pial Surf lh Mon Feb 4 17:03:10 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_make_surfaces -orig orig_white -orig_white orig_white -orig_pial orig_pial -long -max 3.5 -white NOWRITE -mgz -T1 brain.finalsurfs S1326RML1.long.S1326RML lh reading original vertex positions from orig_white -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using orig_white starting white location... using orig_pial starting pial locations... Using longitudinal scheme using max_thickness = 3.5 INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/filled.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/brain.finalsurfs.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/wm.mgz... 6570 bright wm thresholded. 6215 bright non-wm voxels segmented. reading original surface position from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.orig_white... computing class statistics... border white: 252030 voxels (1.50%) border gray 280397 voxels (1.67%) WM (95.0): 95.6 +- 6.8 [70.0 --> 110.0] GM (84.0) : 82.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.1 (was 70) setting MAX_BORDER_WHITE to 109.8 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 51.2 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=73 using class modes intead of means.... mean inside = 93.1, mean outside = 78.6 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.91 +- 0.25 (0.05-->6.65) (max @ vno 59248 --> 59267) face area 0.34 +- 0.16 (0.00-->5.90) mean absolute distance = 0.51 +- 0.74 2448 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 5 with 423 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 25.00% unknown deleting segment 8 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 17 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown mean border=82.9, 186 (185) missing vertices, mean dist 0.2 [0.5 (%28.4)->0.5 (%71.6))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.10-->6.78) (max @ vno 104050 --> 97683) face area 0.34 +- 0.16 (0.00-->7.65) mean absolute distance = 0.32 +- 0.56 2759 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4125637.8, rms=5.88 001: dt: 0.5000, sse=3707618.0, rms=3.79 002: dt: 0.5000, sse=4065848.8, rms=2.86 003: dt: 0.5000, sse=4368408.0, rms=2.51 004: dt: 0.5000, sse=4599089.5, rms=2.38 rms = 2.36, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=4729498.5, rms=2.36 006: dt: 0.2500, sse=3075982.8, rms=1.60 007: dt: 0.2500, sse=2908321.5, rms=1.46 rms = 1.44, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=2839045.0, rms=1.44 rms = 1.42, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=2806229.5, rms=1.42 positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 2 with 399 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 63 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=85.0, 171 (89) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.2 (%31.2))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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 0.92 +- 0.25 (0.08-->6.84) (max @ vno 58235 --> 59267) face area 0.36 +- 0.17 (0.00-->9.02) mean absolute distance = 0.27 +- 0.46 3398 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3067143.8, rms=3.34 010: dt: 0.5000, sse=3325394.8, rms=2.01 011: dt: 0.5000, sse=3581275.8, rms=1.85 rms = 1.81, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=3790604.5, rms=1.81 013: dt: 0.2500, sse=3164747.0, rms=1.30 014: dt: 0.2500, sse=3050022.0, rms=1.22 rms = 1.22, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3003202.5, rms=1.22 rms = 1.20, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=2977680.2, rms=1.20 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 2 with 424 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 28 points - only 0.00% unknown deleting segment 7 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=86.7, 166 (68) missing vertices, mean dist -0.1 [0.3 (%66.5)->0.2 (%33.5))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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 (0.10-->7.02) (max @ vno 58235 --> 59267) face area 0.35 +- 0.17 (0.00-->9.26) mean absolute distance = 0.24 +- 0.37 3288 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3091387.8, rms=2.61 017: dt: 0.5000, sse=3357887.0, rms=1.80 018: dt: 0.5000, sse=3488151.5, rms=1.72 rms = 1.73, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3228067.0, rms=1.36 020: dt: 0.2500, sse=3137333.8, rms=1.17 rms = 1.14, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3112494.5, rms=1.14 rms = 1.13, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3092132.8, rms=1.13 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 427 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown deleting segment 5 with 17 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 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown mean border=87.4, 182 (65) missing vertices, mean dist -0.1 [0.3 (%54.8)->0.2 (%45.2))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3105687.8, rms=1.53 023: dt: 0.5000, sse=3733751.5, rms=1.24 rms = 1.42, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3465411.5, rms=1.04 025: dt: 0.2500, sse=3344554.2, rms=0.98 rms = 0.96, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3368159.0, rms=0.96 rms = 0.95, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3370090.8, rms=0.95 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from orig_pial... mean border=63.2, 322 (322) missing vertices, mean dist 0.2 [0.4 (%41.7)->0.8 (%58.3))] %22 local maxima, %46 large gradients and %27 min vals, 2535 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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=4052991.5, rms=6.77 001: dt: 0.5000, sse=4039014.2, rms=5.03 002: dt: 0.5000, sse=4059951.5, rms=3.95 003: dt: 0.5000, sse=4204087.0, rms=3.32 004: dt: 0.5000, sse=4328591.5, rms=2.99 005: dt: 0.5000, sse=4462433.5, rms=2.88 006: dt: 0.5000, sse=4502267.0, rms=2.79 rms = 2.78, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=4556957.0, rms=2.78 008: dt: 0.2500, sse=3517801.2, rms=2.28 009: dt: 0.2500, sse=3436744.8, rms=2.18 rms = 2.17, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3397523.0, rms=2.17 011: dt: 0.1250, sse=3313184.5, rms=2.10 rms = 2.09, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3307922.2, rms=2.09 positioning took 1.9 minutes mean border=61.7, 1336 (158) missing vertices, mean dist 0.2 [0.2 (%50.3)->0.7 (%49.7))] %36 local maxima, %34 large gradients and %25 min vals, 1722 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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=3576787.2, rms=3.59 013: dt: 0.5000, sse=3778860.8, rms=2.95 014: dt: 0.5000, sse=4500482.0, rms=2.77 rms = 2.76, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=4538009.0, rms=2.76 016: dt: 0.2500, sse=3802759.5, rms=2.24 017: dt: 0.2500, sse=3757822.2, rms=2.11 rms = 2.12, time step reduction 2 of 3 to 0.125... rms = 2.08, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3718245.2, rms=2.08 positioning took 1.1 minutes mean border=60.3, 1694 (131) missing vertices, mean dist 0.1 [0.2 (%42.3)->0.5 (%57.7))] %47 local maxima, %23 large gradients and %24 min vals, 1792 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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=3849709.2, rms=2.96 019: dt: 0.5000, sse=4068057.0, rms=2.75 020: dt: 0.5000, sse=4820691.0, rms=2.64 rms = 2.73, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4195162.5, rms=2.19 022: dt: 0.2500, sse=3988371.8, rms=2.05 rms = 2.04, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3954606.0, rms=2.04 024: dt: 0.1250, sse=3847511.5, rms=1.93 rms = 1.92, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3840075.8, rms=1.92 positioning took 1.2 minutes mean border=59.5, 3629 (120) missing vertices, mean dist 0.1 [0.3 (%45.3)->0.4 (%54.7))] %54 local maxima, %16 large gradients and %23 min vals, 1716 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3876060.0, rms=2.25 rms = 2.28, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=3807615.5, rms=2.07 027: dt: 0.2500, sse=3862444.5, rms=1.94 rms = 1.91, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=3902708.0, rms=1.91 029: dt: 0.1250, sse=3849287.8, rms=1.86 rms = 1.85, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3856317.8, rms=1.85 positioning took 0.9 minutes writing curvature file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.area.pial vertex spacing 1.01 +- 0.42 (0.09-->8.63) (max @ vno 94022 --> 91249) face area 0.41 +- 0.31 (0.00-->17.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 129478 vertices processed 25000 of 129478 vertices processed 50000 of 129478 vertices processed 75000 of 129478 vertices processed 100000 of 129478 vertices processed 125000 of 129478 vertices processed 0 of 129478 vertices processed 25000 of 129478 vertices processed 50000 of 129478 vertices processed 75000 of 129478 vertices processed 100000 of 129478 vertices processed 125000 of 129478 vertices processed thickness calculation complete, 2857:2764 truncations. 50272 vertices at 0 distance 74394 vertices at 1 distance 62968 vertices at 2 distance 33119 vertices at 3 distance 15410 vertices at 4 distance 6541 vertices at 5 distance 2598 vertices at 6 distance 1101 vertices at 7 distance 558 vertices at 8 distance 304 vertices at 9 distance 167 vertices at 10 distance 123 vertices at 11 distance 88 vertices at 12 distance 52 vertices at 13 distance 39 vertices at 14 distance 29 vertices at 15 distance 26 vertices at 16 distance 32 vertices at 17 distance 26 vertices at 18 distance 24 vertices at 19 distance 47 vertices at 20 distance writing curvature file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.thickness positioning took 13.6 minutes #-------------------------------------------- #@# Surf Volume lh Mon Feb 4 17:16:44 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/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_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Mon Feb 4 17:16:45 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab S1326RML1.long.S1326RML lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/wm.mgz... reading input surface /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.white... reading input pial surface /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.pial... reading input white surface /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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 1503 1052 2469 2.452 0.541 0.101 0.021 8 1.3 bankssts 985 682 2371 3.257 0.663 0.140 0.031 13 1.2 caudalanteriorcingulate 3558 2410 6898 2.551 0.685 0.111 0.025 26 3.8 caudalmiddlefrontal 1893 1313 2430 2.027 0.540 0.155 0.045 26 3.3 cuneus 533 391 1690 3.667 0.789 0.170 0.070 8 1.8 entorhinal 4789 3323 11018 2.995 0.840 0.147 0.055 73 9.0 fusiform 5801 3955 12253 2.649 0.951 0.125 0.032 57 7.5 inferiorparietal 4661 3199 11747 3.136 0.823 0.143 0.049 67 9.5 inferiortemporal 1218 813 2764 3.311 0.867 0.152 0.072 24 3.3 isthmuscingulate 8432 5743 14090 2.280 0.742 0.148 0.050 125 16.3 lateraloccipital 4038 2758 9176 3.118 1.031 0.136 0.046 70 7.5 lateralorbitofrontal 4537 3149 7673 2.371 0.751 0.161 0.072 202 11.9 lingual 2574 1709 5371 2.828 1.008 0.135 0.051 43 5.1 medialorbitofrontal 4242 3017 11438 3.136 0.738 0.146 0.048 64 8.5 middletemporal 1106 687 2960 3.529 0.792 0.120 0.059 20 2.4 parahippocampal 2028 1337 3249 2.317 0.551 0.111 0.029 14 2.4 paracentral 1949 1355 3941 2.640 0.634 0.108 0.028 15 2.0 parsopercularis 857 571 2635 3.252 0.961 0.168 0.073 17 2.4 parsorbitalis 1895 1353 4073 2.765 0.723 0.128 0.031 19 2.4 parstriangularis 1233 909 1680 1.928 0.682 0.227 0.219 167 8.6 pericalcarine 5887 3868 8540 1.954 0.757 0.113 0.029 51 7.3 postcentral 1529 1110 3579 3.177 0.638 0.146 0.041 21 2.5 posteriorcingulate 7551 4954 13255 2.430 0.711 0.107 0.026 51 8.2 precentral 4816 3340 8853 2.657 0.781 0.132 0.036 48 6.9 precuneus 1397 888 3076 3.115 0.827 0.145 0.138 52 8.3 rostralanteriorcingulate 8295 5737 18704 2.813 0.883 0.147 0.068 136 26.2 rostralmiddlefrontal 10167 6925 24146 2.963 0.825 0.129 0.036 110 15.1 superiorfrontal 8277 5673 13639 2.160 0.789 0.121 0.030 74 10.3 superiorparietal 5159 3743 12144 2.829 0.807 0.123 0.033 48 7.3 superiortemporal 5349 3733 11273 2.698 0.818 0.138 0.045 65 9.7 supramarginal 374 246 1075 2.953 1.019 0.181 0.084 9 1.4 frontalpole 722 517 2688 3.760 0.886 0.167 0.063 12 1.9 temporalpole 733 473 1180 2.280 0.629 0.119 0.036 6 1.1 transversetemporal 3870 2591 8364 3.186 1.017 0.125 0.107 94 13.6 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Feb 4 17:17:09 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/label/lh.aparc.a2009s.annot S1326RML1.long.S1326RML lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline will refine the initial labeling read-in from -R reading precomputed parcellation from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/label/lh.aparc.a2009s.annot... $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) 000: 2698 changed, 129478 examined... 001: 669 changed, 13140 examined... 002: 180 changed, 4014 examined... 003: 59 changed, 1051 examined... 004: 21 changed, 342 examined... 005: 9 changed, 122 examined... 006: 5 changed, 56 examined... 007: 2 changed, 24 examined... 008: 1 changed, 8 examined... 009: 0 changed, 5 examined... 000: 155 total segments, 68 labels (323 vertices) changed 001: 88 total segments, 1 labels (1 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 63 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 213 vertices marked for relabeling... 213 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 20 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Feb 4 17:18:30 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_anatomical_stats -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 S1326RML1.long.S1326RML lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/wm.mgz... reading input surface /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.white... reading input pial surface /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.pial... reading input white surface /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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 1149 848 2399 2.604 0.856 0.175 0.072 22 3.2 G_and_S_frontomargin 2221 1576 4183 2.419 0.746 0.143 0.040 25 3.4 G_and_S_occipital_inf 1483 917 2359 2.295 0.532 0.121 0.033 14 2.1 G_and_S_paracentral 1384 982 2983 2.752 0.650 0.151 0.043 18 2.4 G_and_S_subcentral 653 457 1936 3.002 0.726 0.182 0.086 17 2.4 G_and_S_transv_frontopol 2394 1644 5071 3.022 0.754 0.132 0.094 59 9.6 G_and_S_cingul-Ant 1524 1077 3081 2.778 0.632 0.124 0.028 14 1.8 G_and_S_cingul-Mid-Ant 1345 948 2826 2.806 0.626 0.122 0.027 13 1.5 G_and_S_cingul-Mid-Post 435 302 1291 3.889 0.651 0.171 0.056 7 1.0 G_cingul-Post-dorsal 177 116 423 2.635 0.761 0.114 0.028 1 0.2 G_cingul-Post-ventral 1768 1245 2433 1.944 0.499 0.157 0.047 24 3.4 G_cuneus 1121 788 3021 2.944 0.589 0.132 0.044 14 1.8 G_front_inf-Opercular 332 211 1109 3.726 0.723 0.135 0.037 3 0.5 G_front_inf-Orbital 1131 801 2813 2.811 0.637 0.147 0.039 16 1.9 G_front_inf-Triangul 4401 2905 12132 2.996 0.845 0.144 0.080 80 18.1 G_front_middle 7229 4753 19204 3.112 0.845 0.137 0.041 92 12.5 G_front_sup 462 290 1199 3.467 1.002 0.099 0.066 6 1.2 G_Ins_lg_and_S_cent_ins 665 378 2065 4.011 1.063 0.116 0.054 10 1.6 G_insular_short 1785 1173 4129 2.749 0.830 0.149 0.047 25 3.4 G_occipital_middle 1633 1119 2359 1.943 0.504 0.131 0.034 16 2.3 G_occipital_sup 1899 1251 4943 3.092 0.792 0.152 0.067 34 3.7 G_oc-temp_lat-fusifor 2693 1824 4576 2.215 0.754 0.164 0.082 98 8.6 G_oc-temp_med-Lingual 1179 751 3560 3.617 0.770 0.131 0.067 23 3.0 G_oc-temp_med-Parahip 2570 1717 6886 2.976 1.035 0.157 0.068 68 6.5 G_orbital 1877 1262 5279 3.177 0.967 0.136 0.039 23 3.1 G_pariet_inf-Angular 3045 2111 7675 2.894 0.794 0.151 0.057 48 6.9 G_pariet_inf-Supramar 2809 1921 6551 2.643 0.886 0.135 0.037 33 4.3 G_parietal_sup 2157 1349 3508 2.069 0.619 0.119 0.033 22 3.0 G_postcentral 3028 1883 6274 2.614 0.695 0.098 0.024 20 3.0 G_precentral 2139 1478 4730 2.737 0.684 0.145 0.044 29 3.7 G_precuneus 1030 650 2613 2.778 0.908 0.156 0.067 24 2.9 G_rectus 844 538 1483 2.651 1.259 0.158 0.180 40 7.2 G_subcallosal 575 379 1020 2.207 0.565 0.115 0.035 5 0.8 G_temp_sup-G_T_transv 1982 1444 5895 2.960 0.751 0.142 0.041 25 3.7 G_temp_sup-Lateral 695 519 1964 3.367 0.893 0.134 0.045 7 1.3 G_temp_sup-Plan_polar 818 596 1759 2.747 0.752 0.095 0.017 4 0.6 G_temp_sup-Plan_tempo 2959 2008 8476 3.250 0.861 0.155 0.057 50 7.1 G_temporal_inf 2699 1921 8701 3.259 0.769 0.158 0.057 52 6.2 G_temporal_middle 231 167 432 2.824 0.452 0.101 0.019 1 0.1 Lat_Fis-ant-Horizont 308 227 503 2.400 0.393 0.086 0.016 1 0.2 Lat_Fis-ant-Vertical 1301 893 1777 2.461 0.558 0.119 0.030 9 1.6 Lat_Fis-post 3059 2117 5334 2.267 0.829 0.186 0.083 168 10.3 Pole_occipital 1749 1223 5740 3.543 0.825 0.176 0.082 41 5.7 Pole_temporal 1598 1086 2362 2.446 0.979 0.178 0.170 154 7.2 S_calcarine 2835 1921 2816 1.607 0.622 0.099 0.022 14 2.6 S_central 1130 815 1851 2.495 0.703 0.117 0.028 7 1.4 S_cingul-Marginalis 418 299 987 3.811 0.541 0.112 0.025 2 0.4 S_circular_insula_ant 1247 931 2438 2.982 0.706 0.093 0.024 7 1.3 S_circular_insula_inf 1907 1332 3439 3.044 0.631 0.113 0.026 12 2.1 S_circular_insula_sup 893 657 1671 2.507 0.790 0.129 0.033 8 1.3 S_collat_transv_ant 502 342 713 2.525 0.588 0.143 0.039 5 0.8 S_collat_transv_post 2214 1563 3124 2.305 0.787 0.114 0.026 15 2.3 S_front_inf 1779 1236 3009 2.705 0.728 0.125 0.035 19 2.4 S_front_middle 2395 1698 4468 2.490 0.702 0.114 0.030 19 3.0 S_front_sup 122 83 352 3.079 0.767 0.138 0.031 1 0.2 S_interm_prim-Jensen 3077 2149 3852 1.825 0.606 0.097 0.020 17 2.5 S_intrapariet_and_P_trans 909 613 1109 2.049 0.671 0.133 0.036 9 1.3 S_oc_middle_and_Lunatus 1319 941 1791 2.341 0.584 0.146 0.036 15 2.0 S_oc_sup_and_transversal 917 646 1177 2.108 0.686 0.109 0.024 5 0.9 S_occipital_ant 1051 727 1812 2.832 0.646 0.136 0.043 10 1.7 S_oc-temp_lat 2387 1686 4395 2.795 0.703 0.126 0.030 19 3.0 S_oc-temp_med_and_Lingual 411 287 636 2.769 0.887 0.134 0.031 3 0.5 S_orbital_lateral 1018 707 1410 2.201 0.809 0.138 0.178 39 2.9 S_orbital_med-olfact 1509 1070 3418 3.454 0.884 0.132 0.037 14 2.5 S_orbital-H_Shaped 2276 1577 3243 2.468 0.780 0.127 0.031 19 2.9 S_parieto_occipital 1306 839 2153 3.215 0.808 0.145 0.061 26 2.7 S_pericallosal 2978 2032 3578 1.881 0.640 0.108 0.027 20 3.2 S_postcentral 1431 982 2263 2.382 0.600 0.100 0.020 8 1.2 S_precentral-inf-part 1600 1123 2160 2.159 0.656 0.103 0.021 9 1.4 S_precentral-sup-part 523 350 972 3.257 1.155 0.106 0.020 3 0.4 S_suborbital 604 414 1281 3.098 0.738 0.131 0.037 6 0.8 S_subparietal 1118 775 2038 3.199 0.713 0.125 0.032 9 1.6 S_temporal_inf 5216 3637 8672 2.485 0.719 0.110 0.025 35 5.2 S_temporal_sup 330 247 559 2.782 0.573 0.148 0.036 4 0.5 S_temporal_transverse #-------------------------------------------- #@# Make White Surf rh Mon Feb 4 17:18:59 EST 2013 cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.white /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.white' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig' cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.white /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig_white `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.white' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig_white' cp -vf /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.pial /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig_pial `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.pial' -> `/prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig_pial' /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_make_surfaces -orig_white orig_white -orig orig_white -long -max 3.5 -noaparc -whiteonly -mgz -T1 brain.finalsurfs S1326RML1.long.S1326RML rh reading original vertex positions from orig_white only generating white matter surface using orig_white starting white location... Using longitudinal scheme using max_thickness = 3.5 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 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/filled.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/brain.finalsurfs.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/wm.mgz... 6958 bright wm thresholded. 6120 bright non-wm voxels segmented. reading original surface position from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig_white... computing class statistics... border white: 252030 voxels (1.50%) border gray 280397 voxels (1.67%) WM (95.0): 95.7 +- 6.7 [70.0 --> 110.0] GM (84.0) : 82.2 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.9 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 49.8 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.91 +- 0.25 (0.05-->4.48) (max @ vno 130871 --> 130872) face area 0.35 +- 0.16 (0.00-->4.72) mean absolute distance = 0.51 +- 0.76 2849 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=72 using class modes intead of means.... mean inside = 92.3, mean outside = 77.5 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=82.2, 131 (131) missing vertices, mean dist 0.2 [0.5 (%31.0)->0.5 (%69.0))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.26 (0.09-->4.77) (max @ vno 130871 --> 130872) face area 0.35 +- 0.17 (0.00-->5.33) mean absolute distance = 0.33 +- 0.59 2870 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4322506.5, rms=6.03 001: dt: 0.5000, sse=3880155.2, rms=3.95 002: dt: 0.5000, sse=4249560.0, rms=2.99 003: dt: 0.5000, sse=4603193.5, rms=2.61 004: dt: 0.5000, sse=4790608.5, rms=2.47 rms = 2.43, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=4961892.5, rms=2.43 006: dt: 0.2500, sse=3241088.0, rms=1.65 007: dt: 0.2500, sse=3046283.0, rms=1.49 rms = 1.46, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=2973915.0, rms=1.46 rms = 1.43, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=2933770.2, rms=1.43 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=84.3, 88 (35) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.2 (%31.2))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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 0.92 +- 0.26 (0.03-->4.79) (max @ vno 130871 --> 130872) face area 0.37 +- 0.17 (0.00-->6.13) mean absolute distance = 0.28 +- 0.46 3462 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3211092.0, rms=3.46 010: dt: 0.5000, sse=3487592.5, rms=2.11 011: dt: 0.5000, sse=3764921.5, rms=1.97 rms = 1.92, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=4003690.0, rms=1.92 013: dt: 0.2500, sse=3299200.8, rms=1.34 014: dt: 0.2500, sse=3174647.8, rms=1.24 rms = 1.24, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3120179.2, rms=1.24 rms = 1.22, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3097813.8, rms=1.22 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.1, 131 (27) missing vertices, mean dist -0.1 [0.3 (%66.9)->0.2 (%33.1))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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 +- 0.26 (0.05-->5.02) (max @ vno 51868 --> 51869) face area 0.36 +- 0.17 (0.00-->6.24) mean absolute distance = 0.24 +- 0.38 3397 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3226870.5, rms=2.72 017: dt: 0.5000, sse=3495738.5, rms=1.84 rms = 1.82, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=3617833.2, rms=1.82 019: dt: 0.2500, sse=3304921.5, rms=1.22 020: dt: 0.2500, sse=3246598.8, rms=1.15 rms = 1.14, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3206967.5, rms=1.14 rms = 1.13, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3183664.0, rms=1.13 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.8, 144 (21) missing vertices, mean dist -0.1 [0.3 (%55.1)->0.2 (%44.9))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3196701.5, rms=1.52 023: dt: 0.5000, sse=3894799.8, rms=1.24 rms = 1.48, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3596477.8, rms=1.03 025: dt: 0.2500, sse=3454237.2, rms=0.97 rms = 0.94, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3496980.8, rms=0.94 rms = 0.94, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3487503.0, rms=0.94 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 2413 vertices erasing segment 1 (vno[0] = 54363) erasing segment 2 (vno[0] = 71597) erasing segment 3 (vno[0] = 81709) erasing segment 4 (vno[0] = 86932) erasing segment 5 (vno[0] = 91670) erasing segment 6 (vno[0] = 93649) erasing segment 7 (vno[0] = 93733) erasing segment 8 (vno[0] = 97660) erasing segment 9 (vno[0] = 97741) erasing segment 10 (vno[0] = 101249) erasing segment 11 (vno[0] = 103976) erasing segment 12 (vno[0] = 103995) erasing segment 13 (vno[0] = 104017) writing cortex label to /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/label/rh.cortex.label... LabelWrite: saving to /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/label/rh.cortex.label writing curvature file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.curv writing smoothed area to rh.area writing curvature file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.area vertex spacing 0.91 +- 0.26 (0.05-->5.09) (max @ vno 51868 --> 51869) face area 0.35 +- 0.17 (0.00-->6.19) refinement took 7.2 minutes #-------------------------------------------- #@# Smooth2 rh Mon Feb 4 17:26:15 EST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts 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 rh Mon Feb 4 17:26:21 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 48.1 mm, total surface area = 83937 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.108 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.030 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.9 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 275 vertices thresholded to be in k1 ~ [-0.26 0.64], k2 ~ [-0.09 0.06] total integrated curvature = 0.605*4pi (7.608) --> 0 handles ICI = 1.6, FI = 11.2, variation=187.418 150 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 149 vertices thresholded to be in [-0.14 0.32] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.026 done. #----------------------------------------- #@# Curvature Stats rh Mon Feb 4 17:29:28 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm S1326RML1.long.S1326RML 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 [ S1326RML1.long.S1326RML/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 [ 263 ] Gb_filter = 0 WARN: S lookup min: -0.091733 WARN: S explicit min: 0.000000 vertex = 4 #-------------------------------------------- #@# Sphere rh Mon Feb 4 17:29:37 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts cp /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.sphere /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.sphere #-------------------------------------------- #@# Surf Reg rh Mon Feb 4 17:29:37 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_register -curv -nosulc -norot /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.sphere.reg /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif... will not use the sulcal depth map will not rigidly align the surface writing registered surface to ../surf/rh.sphere.reg... curvature mean = -0.021, std = 0.241 curvature mean = 0.005, std = 0.069 curvature mean = 0.021, std = 0.451 curvature mean = 0.005, std = 0.084 curvature mean = 0.020, std = 0.629 curvature mean = 0.005, std = 0.091 curvature mean = 0.011, std = 0.765 curvature mean = 0.005, std = 0.093 curvature mean = 0.004, std = 0.858 #-------------------------------------------- #@# Jacobian white rh Mon Feb 4 17:47:30 EST 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Mon Feb 4 17:47:34 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mrisp_paint -a 5 /opt/freesurfer/average/rh.average.curvature.filled.buckner40.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.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Mon Feb 4 17:47:37 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/label/rh.aparc.annot S1326RML1.long.S1326RML rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline will refine the initial labeling read-in from -R reading precomputed parcellation from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML/label/rh.aparc.annot... $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) 000: 1135 changed, 131542 examined... 001: 260 changed, 5733 examined... 002: 56 changed, 1595 examined... 003: 21 changed, 344 examined... 004: 10 changed, 125 examined... 005: 3 changed, 58 examined... 006: 2 changed, 22 examined... 007: 1 changed, 14 examined... 008: 2 changed, 7 examined... 009: 0 changed, 8 examined... 000: 62 total segments, 10 labels (10 vertices) changed 001: 52 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 603 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 17 seconds. #-------------------------------------------- #@# Make Pial Surf rh Mon Feb 4 17:48:53 EST 2013 /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts mris_make_surfaces -orig orig_white -orig_white orig_white -orig_pial orig_pial -long -max 3.5 -white NOWRITE -mgz -T1 brain.finalsurfs S1326RML1.long.S1326RML rh reading original vertex positions from orig_white -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using orig_white starting white location... using orig_pial starting pial locations... Using longitudinal scheme using max_thickness = 3.5 INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/filled.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/brain.finalsurfs.mgz... reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/wm.mgz... 6958 bright wm thresholded. 6120 bright non-wm voxels segmented. reading original surface position from /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/surf/rh.orig_white... computing class statistics... border white: 252030 voxels (1.50%) border gray 280397 voxels (1.67%) WM (95.0): 95.7 +- 6.7 [70.0 --> 110.0] GM (84.0) : 82.2 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.9 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 49.8 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.7 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=72 using class modes intead of means.... mean inside = 92.3, mean outside = 77.5 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.91 +- 0.25 (0.05-->4.48) (max @ vno 130871 --> 130872) face area 0.35 +- 0.16 (0.00-->4.72) mean absolute distance = 0.51 +- 0.76 2885 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 387 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=82.2, 131 (131) missing vertices, mean dist 0.2 [0.5 (%30.9)->0.5 (%69.1))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.26 (0.09-->4.77) (max @ vno 130871 --> 130872) face area 0.35 +- 0.16 (0.00-->5.33) mean absolute distance = 0.33 +- 0.59 2884 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4329134.5, rms=6.03 001: dt: 0.5000, sse=3889608.2, rms=3.94 002: dt: 0.5000, sse=4259060.5, rms=2.99 003: dt: 0.5000, sse=4613742.5, rms=2.61 004: dt: 0.5000, sse=4800368.5, rms=2.47 rms = 2.42, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=4972272.5, rms=2.42 006: dt: 0.2500, sse=3246843.2, rms=1.65 007: dt: 0.2500, sse=3051976.0, rms=1.49 rms = 1.46, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=2979659.0, rms=1.46 rms = 1.43, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=2939422.8, rms=1.43 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 3 with 343 points - only 0.00% unknown deleting segment 4 with 64 points - only 50.00% unknown mean border=84.3, 105 (45) missing vertices, mean dist -0.2 [0.4 (%68.9)->0.2 (%31.1))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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 0.92 +- 0.26 (0.03-->4.79) (max @ vno 130871 --> 130872) face area 0.37 +- 0.17 (0.00-->6.13) mean absolute distance = 0.28 +- 0.46 3469 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3220188.8, rms=3.46 010: dt: 0.5000, sse=3495913.0, rms=2.11 011: dt: 0.5000, sse=3776635.8, rms=1.97 rms = 1.93, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=4013939.2, rms=1.93 013: dt: 0.2500, sse=3309113.8, rms=1.34 014: dt: 0.2500, sse=3183909.2, rms=1.25 rms = 1.24, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3129064.5, rms=1.24 rms = 1.22, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3107288.0, rms=1.22 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 2 with 388 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown mean border=86.1, 147 (33) missing vertices, mean dist -0.1 [0.3 (%66.8)->0.2 (%33.2))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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 +- 0.26 (0.05-->5.02) (max @ vno 51868 --> 51869) face area 0.36 +- 0.17 (0.00-->6.24) mean absolute distance = 0.24 +- 0.38 3402 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3236653.5, rms=2.72 017: dt: 0.5000, sse=3505042.8, rms=1.84 rms = 1.82, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=3627378.2, rms=1.82 019: dt: 0.2500, sse=3314180.8, rms=1.22 020: dt: 0.2500, sse=3255394.2, rms=1.15 rms = 1.14, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3215119.5, rms=1.14 rms = 1.13, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3191677.0, rms=1.13 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 2 with 397 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown mean border=86.8, 161 (26) missing vertices, mean dist -0.1 [0.3 (%55.1)->0.2 (%44.9))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3204823.8, rms=1.52 023: dt: 0.5000, sse=3904668.2, rms=1.24 rms = 1.47, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3605682.5, rms=1.03 025: dt: 0.2500, sse=3463230.8, rms=0.97 rms = 0.94, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3506517.8, rms=0.94 rms = 0.94, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3496694.8, rms=0.94 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from orig_pial... mean border=62.1, 445 (445) missing vertices, mean dist 0.2 [0.4 (%41.3)->0.8 (%58.7))] %24 local maxima, %44 large gradients and %28 min vals, 2210 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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=4156860.2, rms=6.46 001: dt: 0.5000, sse=4127877.8, rms=4.69 002: dt: 0.5000, sse=4261187.0, rms=3.76 003: dt: 0.5000, sse=4476119.0, rms=3.27 004: dt: 0.5000, sse=4635930.5, rms=3.05 005: dt: 0.5000, sse=4735731.0, rms=2.96 006: dt: 0.5000, sse=4828143.5, rms=2.89 rms = 2.87, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=4850564.5, rms=2.87 008: dt: 0.2500, sse=3727042.2, rms=2.39 009: dt: 0.2500, sse=3620150.0, rms=2.30 rms = 2.28, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3589857.2, rms=2.28 011: dt: 0.1250, sse=3488501.0, rms=2.23 rms = 2.23, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3478425.5, rms=2.23 positioning took 2.0 minutes mean border=60.4, 1607 (287) missing vertices, mean dist 0.2 [0.2 (%49.2)->0.7 (%50.8))] %36 local maxima, %32 large gradients and %26 min vals, 1353 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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 Linux hhlxnrcas26 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s S1326RML1.long.S1326RML exited with ERRORS at Mon Feb 4 18:03:42 EST 2013 For more details, see the log file /prod2/allegra/barcslong_t1/SUBJECTS/S1326RML1.long.S1326RML/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting