Dear FreeSurfer experts, I am using HCP pipelines with my custom modifications of FreeSurferHiResWhite.sh (especially to accomodate full-hires reconstruction) to generate white and pial surfaces.
I tested the v6.0 beta mris_make_surfaces binary to hopefully fix some problems with surfaces I found previously with 5.3.0_HCP version. This update helped to fix my problems but I found that with v.6.0 there is a new issue with overlaping pial surfaces in hemispherical region. This issue is not present in 5.3.0 version of mris_make_surfaces. My command line is mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm wm.hires -mgz -sdir my_subject_dir -orig white.deformed -nowhite -orig_white white.deformed -orig_pial pial -T2 my_subj/mri/T2w_hires.norm -T1 T1w_hires_norm my_subject_id lh The previous invocation of mris_make_surfaces in FreeSurferHiResWhite.sh (which does not use T2 refinement): mris_make_surfaces -variablesigma 4 -white NOWRITE -aseg aseg.hires -orig white.deformed -filled filled.hires -wm wm.hires -sdir my_subject_dir -mgz -T1 T1w_hires_norm my_subject_id lh produces surfaces which do not overlap. It seems to me that -aseg option of mris_make_surfaces (preventing surfaces to crossing the midline) is not active in case of -T2 refinement. I also tried to add -white NOWRITE or -cover_seg parameters, but it did not helped either. See attached screenshot aseg.hires overlaid with surfaces: blue are surfaces without T2 refinement (without interhemispheric overlap), yellow are surfaces after T2 refinement (with interhemispheric overlap). Attached is also the log file of my mris_make_surfaces -T2 command. I also uploaded the subject overlapping_surfs.tar.gz to your FTP file exchange server. Regards, Antonin Skoch
using T2 threshold of 2.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using filled.hires as filled name using wm.hires as filled name reading original vertex positions from white.deformed reading previously compute gray/white surface refining pial surfaces placement using T2 volume HCE_C00612_20160322_1220_1_base/mri/T2w_hires.norm appending postT2.pass2.pok_fs_v6beta to output names... using aseg volume aseg.hires to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long as SUBJECTS_DIR... using white.deformed starting white location... using pial.preT2.pass2 starting pial locations... using T1w_hires.norm as T1 volume... $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ $Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $ reading volume /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/mri/filled.hires.mgz... reading volume /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/mri/T1w_hires.norm.mgz... reading volume /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/mri/aseg.hires.mgz... reading volume /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/mri/wm.hires.mgz... 403421 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/surf/lh.white.deformed... computing class statistics... border white: 585292 voxels (1.95%) border gray 609664 voxels (2.03%) WM (101.0): 100.0 +- 7.6 [70.0 --> 110.0] GM (80.0) : 80.0 +- 9.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.6 (was 70) setting MAX_BORDER_WHITE to 117.6 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 57.3 (was 40) setting MAX_GRAY to 102.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.9 (was 40) resampling filled volume to be in voxel register with T1 changing type of input wm volume to UCHAR... resampling wm volume to be in voxel register with T1 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=110+-7.0, GM=76+-4.3 mean inside = 101.0, mean outside = 81.6 reading initial white vertex positions from white.deformed... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white.deformed... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 54 points - only 0.00% unknown deleting segment 1 with 45 points - only 0.00% unknown deleting segment 2 with 206 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown reading initial pial vertex positions from pial.preT2.pass2... repositioning pial surface locations using HCE_C00612_20160322_1220_1_base/mri/T2w_hires.norm.mgz (box.dx, box.dy, box.dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (box.dx, box.dy, box.dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) locating cortical regions not in the range [65.61 108.18], gm=91.15+-8.51, and vertices in regions > 86.9 235192 surface locations found to contain inconsistent values (106885 in, 128307 out) perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.05 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=140879.9, rms=0.355 001: dt: 0.0500, sse=140487.1, rms=0.353 (0.624%) 002: dt: 0.0500, sse=140027.3, rms=0.351 (0.729%) 003: dt: 0.0500, sse=139583.5, rms=0.348 (0.705%) 004: dt: 0.0500, sse=139156.0, rms=0.346 (0.691%) 005: dt: 0.0500, sse=138735.5, rms=0.343 (0.683%) 006: dt: 0.0500, sse=138325.0, rms=0.341 (0.673%) 007: dt: 0.0500, sse=137925.7, rms=0.339 (0.662%) 008: dt: 0.0500, sse=137534.3, rms=0.337 (0.654%) 009: dt: 0.0500, sse=137152.9, rms=0.335 (0.643%) 010: dt: 0.0500, sse=136780.1, rms=0.332 (0.634%) positioning took 2.2 minutes mean border=63.0, 9463 (0) missing vertices, mean dist -0.1 [0.3 (%86.6)->0.8 (%13.4))] %25 local maxima, %40 large gradients and %27 min vals, 13 gradients ignored tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=136205.5, rms=0.332 011: dt: 0.0500, sse=135842.5, rms=0.330 (0.625%) 012: dt: 0.0500, sse=135488.2, rms=0.328 (0.614%) 013: dt: 0.0500, sse=135142.8, rms=0.326 (0.605%) 014: dt: 0.0500, sse=134804.2, rms=0.324 (0.596%) 015: dt: 0.0500, sse=134475.0, rms=0.322 (0.587%) 016: dt: 0.0500, sse=134152.6, rms=0.321 (0.579%) 017: dt: 0.0500, sse=133839.1, rms=0.319 (0.570%) 018: dt: 0.0500, sse=133533.1, rms=0.317 (0.561%) 019: dt: 0.0500, sse=133234.4, rms=0.315 (0.553%) 020: dt: 0.0500, sse=132944.0, rms=0.313 (0.542%) positioning took 2.2 minutes mean border=63.0, 9654 (0) missing vertices, mean dist -0.1 [0.3 (%84.1)->0.7 (%15.9))] %25 local maxima, %40 large gradients and %27 min vals, 18 gradients ignored tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.05 000: dt: 0.0000, sse=132621.2, rms=0.313 021: dt: 0.0500, sse=132336.8, rms=0.312 (0.534%) 022: dt: 0.0500, sse=132059.7, rms=0.310 (0.526%) 023: dt: 0.0500, sse=131789.2, rms=0.309 (0.518%) 024: dt: 0.0500, sse=131525.8, rms=0.307 (0.509%) 025: dt: 0.0500, sse=131269.3, rms=0.305 (0.500%) 026: dt: 0.0500, sse=131018.8, rms=0.304 (0.493%) 027: dt: 0.0500, sse=130774.5, rms=0.302 (0.485%) 028: dt: 0.0500, sse=130536.4, rms=0.301 (0.477%) 029: dt: 0.0500, sse=130303.9, rms=0.300 (0.470%) 030: dt: 0.0500, sse=130076.8, rms=0.298 (0.463%) positioning took 2.2 minutes mean border=63.0, 9832 (0) missing vertices, mean dist -0.1 [0.3 (%81.2)->0.6 (%18.8))] %25 local maxima, %40 large gradients and %27 min vals, 19 gradients ignored tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=129877.3, rms=0.298 031: dt: 0.5000, sse=127798.2, rms=0.286 (4.270%) 032: dt: 0.5000, sse=126159.9, rms=0.275 (3.738%) 033: dt: 0.5000, sse=124730.8, rms=0.265 (3.437%) 034: dt: 0.5000, sse=123561.6, rms=0.257 (3.010%) 035: dt: 0.5000, sse=122576.2, rms=0.251 (2.678%) 036: dt: 0.5000, sse=121768.8, rms=0.245 (2.317%) 037: dt: 0.5000, sse=121063.0, rms=0.240 (2.111%) 038: dt: 0.5000, sse=120467.6, rms=0.235 (1.858%) 039: dt: 0.5000, sse=119951.0, rms=0.231 (1.654%) 040: dt: 0.5000, sse=119510.6, rms=0.228 (1.469%) 041: dt: 0.5000, sse=119130.8, rms=0.225 (1.297%) 042: dt: 0.5000, sse=118813.0, rms=0.222 (1.127%) 043: dt: 0.5000, sse=118523.8, rms=0.220 (1.023%) 044: dt: 0.5000, sse=118274.7, rms=0.218 (0.928%) 045: dt: 0.5000, sse=118064.3, rms=0.216 (0.794%) 046: dt: 0.5000, sse=117882.5, rms=0.215 (0.719%) 047: dt: 0.5000, sse=117721.3, rms=0.213 (0.641%) 048: dt: 0.5000, sse=117578.6, rms=0.212 (0.570%) 049: dt: 0.5000, sse=117462.1, rms=0.211 (0.489%) 050: dt: 0.5000, sse=117348.8, rms=0.210 (0.461%) 051: dt: 0.5000, sse=117258.2, rms=0.209 (0.380%) 052: dt: 0.5000, sse=117181.3, rms=0.209 (0.342%) 053: dt: 0.5000, sse=117114.7, rms=0.208 (0.292%) 054: dt: 0.5000, sse=117053.4, rms=0.207 (0.274%) 055: dt: 0.5000, sse=117003.7, rms=0.207 (0.236%) 056: dt: 0.5000, sse=116962.9, rms=0.206 (0.206%) 057: dt: 0.5000, sse=116930.9, rms=0.206 (0.162%) 058: dt: 0.5000, sse=116903.7, rms=0.206 (0.146%) 059: dt: 0.5000, sse=116879.9, rms=0.206 (0.128%) 060: dt: 0.5000, sse=116869.3, rms=0.205 (0.087%) positioning took 6.6 minutes repositioning pial surface locations using HCE_C00612_20160322_1220_1_base/mri/T2w_hires.norm.mgz (box.dx, box.dy, box.dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (box.dx, box.dy, box.dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) locating cortical regions not in the range [64.71 108.78], gm=91.15+-8.81, and vertices in regions > 86.7 211921 surface locations found to contain inconsistent values (27196 in, 184725 out) tol=1.0e-04, sigma=1.0, host=unkno, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=121681.4, rms=0.245 061: dt: 0.5000, sse=121024.0, rms=0.239 (2.572%) 062: dt: 0.5000, sse=120161.0, rms=0.233 (2.725%) 063: dt: 0.5000, sse=119646.1, rms=0.229 (1.647%) 064: dt: 0.5000, sse=119283.5, rms=0.226 (1.243%) 065: dt: 0.5000, sse=118954.1, rms=0.223 (1.126%) 066: dt: 0.5000, sse=118672.9, rms=0.221 (0.979%) 067: dt: 0.5000, sse=118430.1, rms=0.219 (0.844%) 068: dt: 0.5000, sse=118222.5, rms=0.218 (0.732%) 069: dt: 0.5000, sse=118046.1, rms=0.216 (0.630%) 070: dt: 0.5000, sse=117894.5, rms=0.215 (0.539%) 071: dt: 0.5000, sse=117763.6, rms=0.214 (0.473%) 072: dt: 0.5000, sse=117653.4, rms=0.213 (0.400%) 073: dt: 0.5000, sse=117561.0, rms=0.213 (0.353%) 074: dt: 0.5000, sse=117477.2, rms=0.212 (0.318%) 075: dt: 0.5000, sse=117407.9, rms=0.211 (0.254%) 076: dt: 0.5000, sse=117344.4, rms=0.211 (0.233%) 077: dt: 0.5000, sse=117291.7, rms=0.210 (0.215%) 078: dt: 0.5000, sse=117247.0, rms=0.210 (0.180%) 079: dt: 0.5000, sse=117208.7, rms=0.210 (0.160%) 080: dt: 0.5000, sse=117171.0, rms=0.209 (0.137%) 081: dt: 0.5000, sse=117145.1, rms=0.209 (0.123%) 082: dt: 0.5000, sse=117121.5, rms=0.209 (0.106%) 083: dt: 0.5000, sse=117101.3, rms=0.209 (0.094%) 084: dt: 0.5000, sse=117083.9, rms=0.209 (0.075%) 085: dt: 0.5000, sse=117066.8, rms=0.208 (0.066%) 086: dt: 0.5000, sse=117059.5, rms=0.208 (0.050%) 087: dt: 0.5000, sse=117050.8, rms=0.208 (0.056%) 088: dt: 0.5000, sse=117041.4, rms=0.208 (0.054%) 089: dt: 0.5000, sse=117040.5, rms=0.208 (0.024%) 090: dt: 0.5000, sse=117033.0, rms=0.208 (0.050%) positioning took 6.7 minutes repositioning pial surface locations using HCE_C00612_20160322_1220_1_base/mri/T2w_hires.norm.mgz (box.dx, box.dy, box.dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (box.dx, box.dy, box.dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) locating cortical regions not in the range [64.71 108.78], gm=91.15+-8.81, and vertices in regions > 86.7 207400 surface locations found to contain inconsistent values (31767 in, 175633 out) tol=1.0e-04, sigma=0.5, host=unkno, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=122305.2, rms=0.236 091: dt: 0.5000, sse=121845.7, rms=0.231 (2.126%) 092: dt: 0.5000, sse=121198.1, rms=0.226 (2.091%) 093: dt: 0.5000, sse=120795.8, rms=0.223 (1.267%) 094: dt: 0.5000, sse=120496.6, rms=0.221 (1.008%) 095: dt: 0.5000, sse=120251.9, rms=0.219 (0.837%) 096: dt: 0.5000, sse=120044.0, rms=0.217 (0.719%) 097: dt: 0.5000, sse=119876.3, rms=0.216 (0.585%) 098: dt: 0.5000, sse=119737.6, rms=0.215 (0.483%) 099: dt: 0.5000, sse=119621.5, rms=0.214 (0.399%) 100: dt: 0.5000, sse=119531.4, rms=0.214 (0.322%) 101: dt: 0.5000, sse=119455.6, rms=0.213 (0.263%) 102: dt: 0.5000, sse=119387.8, rms=0.212 (0.247%) 103: dt: 0.5000, sse=119335.1, rms=0.212 (0.193%) 104: dt: 0.5000, sse=119286.4, rms=0.212 (0.176%) 105: dt: 0.5000, sse=119247.4, rms=0.211 (0.148%) 106: dt: 0.5000, sse=119212.8, rms=0.211 (0.125%) 107: dt: 0.5000, sse=119180.5, rms=0.211 (0.116%) 108: dt: 0.5000, sse=119153.9, rms=0.211 (0.099%) 109: dt: 0.5000, sse=119127.3, rms=0.210 (0.087%) 110: dt: 0.5000, sse=119115.1, rms=0.210 (0.064%) 111: dt: 0.5000, sse=119096.3, rms=0.210 (0.054%) 112: dt: 0.5000, sse=119087.6, rms=0.210 (0.045%) 113: dt: 0.5000, sse=119075.1, rms=0.210 (0.053%) 114: dt: 0.5000, sse=119063.1, rms=0.210 (0.049%) 115: dt: 0.5000, sse=119051.7, rms=0.210 (0.052%) 116: dt: 0.5000, sse=119044.6, rms=0.210 (0.037%) 117: dt: 0.5000, sse=119035.9, rms=0.210 (0.037%) 118: dt: 0.5000, sse=119027.5, rms=0.210 (0.033%) 119: dt: 0.5000, sse=119021.1, rms=0.210 (0.027%) 120: dt: 0.5000, sse=119018.8, rms=0.209 (0.026%) positioning took 6.5 minutes repositioning pial surface locations using HCE_C00612_20160322_1220_1_base/mri/T2w_hires.norm.mgz (box.dx, box.dy, box.dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (region->dx, region->dy, region->dz) = (187, 489, 321) (box.dx, box.dy, box.dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) (region->dx, region->dy, region->dz) = (199, 505, 340) locating cortical regions not in the range [64.71 108.78], gm=91.15+-8.81, and vertices in regions > 86.7 203974 surface locations found to contain inconsistent values (26020 in, 177954 out) tol=1.0e-04, sigma=0.2, host=unkno, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 writing pial surface to /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/surf/lh.pialpostT2.pass2.pok_fs_v6beta... writing smoothed curvature to lh.curv.pialpostT2.pass2.pok_fs_v6beta 000: dt: 0.0000, sse=123080.2, rms=0.235 121: dt: 0.5000, sse=122694.0, rms=0.230 (1.839%) 122: dt: 0.5000, sse=122089.5, rms=0.226 (1.773%) 123: dt: 0.5000, sse=121708.5, rms=0.224 (1.132%) 124: dt: 0.5000, sse=121410.7, rms=0.222 (0.930%) 125: dt: 0.5000, sse=121160.8, rms=0.220 (0.774%) 126: dt: 0.5000, sse=120945.6, rms=0.219 (0.670%) 127: dt: 0.5000, sse=120770.6, rms=0.217 (0.556%) 128: dt: 0.5000, sse=120624.1, rms=0.216 (0.466%) 129: dt: 0.5000, sse=120502.8, rms=0.215 (0.384%) 130: dt: 0.5000, sse=120398.7, rms=0.215 (0.336%) 131: dt: 0.5000, sse=120310.4, rms=0.214 (0.277%) 132: dt: 0.5000, sse=120231.2, rms=0.214 (0.253%) 133: dt: 0.5000, sse=120160.9, rms=0.213 (0.217%) 134: dt: 0.5000, sse=120106.7, rms=0.213 (0.175%) 135: dt: 0.5000, sse=120056.4, rms=0.212 (0.162%) 136: dt: 0.5000, sse=120013.2, rms=0.212 (0.137%) 137: dt: 0.5000, sse=119973.4, rms=0.212 (0.114%) 138: dt: 0.5000, sse=119939.8, rms=0.212 (0.108%) 139: dt: 0.5000, sse=119916.1, rms=0.212 (0.086%) 140: dt: 0.5000, sse=119892.9, rms=0.211 (0.083%) 141: dt: 0.5000, sse=119872.7, rms=0.211 (0.075%) 142: dt: 0.5000, sse=119853.0, rms=0.211 (0.074%) 143: dt: 0.5000, sse=119836.1, rms=0.211 (0.052%) 144: dt: 0.5000, sse=119825.3, rms=0.211 (0.043%) 145: dt: 0.5000, sse=119807.0, rms=0.211 (0.046%) 146: dt: 0.5000, sse=119798.6, rms=0.211 (0.036%) 147: dt: 0.5000, sse=119789.5, rms=0.211 (0.042%) 148: dt: 0.5000, sse=119780.2, rms=0.210 (0.033%) 149: dt: 0.5000, sse=119772.5, rms=0.210 (0.028%) 150: dt: 0.5000, sse=119765.4, rms=0.210 (0.031%) positioning took 6.4 minutes writing curvature file /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/surf/lh.curv.pialpostT2.pass2.pok_fs_v6beta writing smoothed area to lh.area.pialpostT2.pass2.pok_fs_v6beta writing curvature file /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/surf/lh.area.pialpostT2.pass2.pok_fs_v6beta vertex spacing 0.75 +- 0.36 (0.01-->6.42) (max @ vno 185577 --> 183914) face area 0.21 +- 0.18 (0.00-->4.89) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 290273 vertices processed 25000 of 290273 vertices processed 50000 of 290273 vertices processed 75000 of 290273 vertices processed 100000 of 290273 vertices processed 125000 of 290273 vertices processed 150000 of 290273 vertices processed 175000 of 290273 vertices processed 200000 of 290273 vertices processed 225000 of 290273 vertices processed 250000 of 290273 vertices processed 275000 of 290273 vertices processed 0 of 290273 vertices processed 25000 of 290273 vertices processed 50000 of 290273 vertices processed 75000 of 290273 vertices processed 100000 of 290273 vertices processed 125000 of 290273 vertices processed 150000 of 290273 vertices processed 175000 of 290273 vertices processed 200000 of 290273 vertices processed 225000 of 290273 vertices processed 250000 of 290273 vertices processed 275000 of 290273 vertices processed thickness calculation complete, 145:934 truncations. 53912 vertices at 0 distance 161405 vertices at 1 distance 169581 vertices at 2 distance 96770 vertices at 3 distance 42246 vertices at 4 distance 16909 vertices at 5 distance 6635 vertices at 6 distance 2705 vertices at 7 distance 1126 vertices at 8 distance 500 vertices at 9 distance 259 vertices at 10 distance 137 vertices at 11 distance 111 vertices at 12 distance 85 vertices at 13 distance 64 vertices at 14 distance 38 vertices at 15 distance 46 vertices at 16 distance 42 vertices at 17 distance 39 vertices at 18 distance 39 vertices at 19 distance 35 vertices at 20 distance writing curvature file /hydra-db/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/HCE_C00612_20160322_1220_1_base/surf/lh.thicknesspostT2.pass2.pok_fs_v6beta positioning took 60.0 minutes
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