External Email - Use Caution
Hi, Douglas,
Thank you for your reply.
I tried adding -max XXX.
If I set the "-max 5" as the default values, the mris_mask_surfaces
would finish running.
However, if I set the "-max" more than 5, the mris_mask_surfaces would
crash during the running - *Segmentation fault (core dumped).*
*This is my computer config:*
*1) Freesurfer Version -
*freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Linux Mint 19.2
3) uname -a: Linux 4.15.0-60-generic #67-Ubuntu SMP Thu Aug 22
16:55:30 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
*Here is the error msg (at the end)for example:*
$mris_make_surfaces -max 10 -max_csf 0.1 -min_gray_at_csf_border 1
-orig_wm orig -noaseg -noaparc -T1 ceb_sm marmosetceb_v2 rh
using max_thickness = 10.0
reading original vertex positions from orig
not using aseg volume to prevent surfaces crossing the midline
not using aparc to prevent surfaces crossing the midline
using ceb_sm as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume
/home/cirong/bin/freesurfer/subjects/marmosetceb_v2/mri/filled.mgz...
reading volume
/home/cirong/bin/freesurfer/subjects/marmosetceb_v2/mri/ceb_sm.mgz...
resampling filled volume to be in voxel register with T1
reading volume
/home/cirong/bin/freesurfer/subjects/marmosetceb_v2/mri/wm.mgz...
changing type of input wm volume to UCHAR...
resampling wm volume to be in voxel register with T1
0 bright wm thresholded.
0 bright non-wm voxels segmented.
reading original surface position from
/home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.orig...
computing class statistics...
border white: 170215 voxels (0.34%)
border gray 211849 voxels (0.42%)
WM (79.0): 80.8 +- 7.5 [70.0 --> 106.0]
GM (71.0) : 71.9 +- 8.9 [30.0 --> 105.0]
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=70+-10.4, GM=69+-10.4
setting MIN_GRAY_AT_WHITE_BORDER to 60.1 (was 70)
setting MAX_BORDER_WHITE to 77.5 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 8.0 (was 40)
setting MAX_GRAY to 62.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 60.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 8.0 (was 40)
mean inside = 74.8, mean outside = 73.4
smoothing surface for 5 iterations...
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.87 +- 0.21 (0.01-->1.75) (max @ vno 190205 --> 190741)
face area 0.31 +- 0.12 (0.00-->0.93)
mean border=73.1, 45600 (45600) missing vertices, mean dist 2.1 [3.9
(%15.7)->2.6 (%84.3))]
%31 local maxima, %44 large gradients and % 2 min vals, 0 gradients
ignored
mean absolute distance = 2.85 +- 2.92
7642 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
tol=1.0e-04, sigma=2.0, host=unkno, nav=4, nbrs=2, l_repulse=5.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=2428827.0, rms=6.800
001: dt: 0.5000, sse=2228267.0, rms=6.217 (8.575%)
002: dt: 0.5000, sse=2028263.5, rms=5.645 (9.199%)
003: dt: 0.5000, sse=1886400.0, rms=5.096 (9.731%)
004: dt: 0.5000, sse=1814327.0, rms=4.583 (10.072%)
005: dt: 0.5000, sse=1721364.9, rms=4.121 (10.063%)
006: dt: 0.5000, sse=1625707.9, rms=3.724 (9.648%)
007: dt: 0.5000, sse=1655070.8, rms=3.394 (8.851%)
008: dt: 0.5000, sse=1652526.4, rms=3.136 (7.621%)
009: dt: 0.5000, sse=1610117.9, rms=2.940 (6.224%)
010: dt: 0.5000, sse=1561510.9, rms=2.795 (4.945%)
011: dt: 0.5000, sse=1554297.9, rms=2.681 (4.083%)
012: dt: 0.5000, sse=1584733.6, rms=2.592 (3.329%)
013: dt: 0.5000, sse=1583861.1, rms=2.517 (2.880%)
014: dt: 0.5000, sse=1546283.4, rms=2.452 (2.578%)
015: dt: 0.5000, sse=1573124.0, rms=2.396 (2.291%)
016: dt: 0.5000, sse=1560157.1, rms=2.343 (2.203%)
rms = 2.30, time step reduction 1 of 3 to 0.250...
017: dt: 0.5000, sse=1584955.1, rms=2.296 (2.021%)
rms = 2.27, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=1413241.2, rms=2.266 (1.279%)
rms = 2.25, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=1348002.0, rms=2.251 (0.692%)
positioning took 2.0 minutes
smoothing T1 volume with sigma = 1.000
vertex spacing 0.81 +- 0.26 (0.02-->3.05) (max @ vno 1015 --> 1374)
face area 0.31 +- 0.17 (0.00-->2.54)
mean border=73.2, 37029 (33580) missing vertices, mean dist -0.4 [1.3
(%54.3)->0.9 (%45.7))]
%45 local maxima, %34 large gradients and % 3 min vals, 0 gradients
ignored
mean absolute distance = 1.13 +- 2.38
7372 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
tol=1.0e-04, sigma=1.0, host=unkno, 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
000: dt: 0.0000, sse=1247019.2, rms=2.658
020: dt: 0.5000, sse=1660886.4, rms=2.513 (5.452%)
021: dt: 0.5000, sse=1696660.5, rms=2.429 (3.370%)
022: dt: 0.5000, sse=1582424.1, rms=2.353 (3.102%)
023: dt: 0.5000, sse=1592837.6, rms=2.296 (2.425%)
024: dt: 0.5000, sse=1575169.2, rms=2.246 (2.202%)
rms = 2.20, time step reduction 1 of 3 to 0.250...
025: dt: 0.5000, sse=1552572.5, rms=2.202 (1.924%)
rms = 2.18, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=1465932.9, rms=2.178 (1.103%)
rms = 2.16, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=1308048.4, rms=2.165 (0.619%)
positioning took 0.9 minutes
smoothing T1 volume with sigma = 0.500
vertex spacing 0.80 +- 0.27 (0.03-->3.21) (max @ vno 1015 --> 1374)
face area 0.26 +- 0.15 (0.00-->2.57)
mean border=73.1, 36657 (30198) missing vertices, mean dist -0.2 [1.2
(%53.9)->0.9 (%46.1))]
%64 local maxima, %15 large gradients and % 2 min vals, 0 gradients
ignored
mean absolute distance = 1.05 +- 1.90
5676 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
tol=1.0e-04, sigma=0.5, host=unkno, 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
000: dt: 0.0000, sse=1326640.1, rms=2.462
028: dt: 0.5000, sse=1621191.5, rms=2.312 (6.099%)
029: dt: 0.5000, sse=1624567.6, rms=2.238 (3.187%)
030: dt: 0.5000, sse=1600156.1, rms=2.183 (2.467%)
rms = 2.14, time step reduction 1 of 3 to 0.250...
031: dt: 0.5000, sse=1617027.1, rms=2.144 (1.794%)
rms = 2.12, time step reduction 2 of 3 to 0.125...
032: dt: 0.2500, sse=1457184.9, rms=2.121 (1.087%)
rms = 2.11, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=1341353.0, rms=2.109 (0.564%)
positioning took 0.7 minutes
smoothing T1 volume with sigma = 0.250
vertex spacing 0.79 +- 0.27 (0.03-->3.02) (max @ vno 166101 --> 167636)
face area 0.25 +- 0.14 (0.00-->2.52)
mean border=73.0, 36288 (28156) missing vertices, mean dist -0.2 [1.0
(%53.1)->0.8 (%46.9))]
%73 local maxima, % 7 large gradients and % 2 min vals, 0 gradients
ignored
mean absolute distance = 0.93 +- 1.64
5026 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
tol=1.0e-04, sigma=0.2, host=unkno, 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
000: dt: 0.0000, sse=1345812.6, rms=2.264
034: dt: 0.5000, sse=1665688.5, rms=2.172 (4.051%)
rms = 2.13, time step reduction 1 of 3 to 0.250...
035: dt: 0.5000, sse=1612717.9, rms=2.133 (1.821%)
rms = 2.11, time step reduction 2 of 3 to 0.125...
036: dt: 0.2500, sse=1435326.8, rms=2.109 (1.107%)
rms = 2.10, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=1305283.9, rms=2.097 (0.555%)
positioning took 0.5 minutes
writing white matter surface to
/home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.white...
writing smoothed curvature to rh.curv
writing curvature file
/home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.curv
writing smoothed area to rh.area
writing curvature file
/home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.area
vertex spacing 0.79 +- 0.27 (0.01-->3.24) (max @ vno 1015 --> 1374)
face area 0.24 +- 0.14 (0.00-->2.12)
smoothing surface for 5 iterations...
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
mean border=46.6, 59907 (59907) missing vertices, mean dist 10.2 [0.0
(%0.0)->14.1 (%100.0))]
%23 local maxima, % 7 large gradients and %41 min vals, 5938 gradients
ignored
averaging target values for 5 iterations...
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=1.000, l_nspring=0.500,
l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=22236570.0, rms=27.443
001: dt: 0.0500, sse=21651240.0, rms=27.069 (1.363%)
002: dt: 0.0500, sse=21290688.0, rms=26.835 (0.862%)
003: dt: 0.0500, sse=21029676.0, rms=26.665 (0.635%)
004: dt: 0.0500, sse=20819052.0, rms=26.527 (0.519%)
005: dt: 0.0500, sse=20636676.0, rms=26.406 (0.454%)
006: dt: 0.0500, sse=20471550.0, rms=26.296 (0.415%)
007: dt: 0.0500, sse=20317400.0, rms=26.194 (0.391%)
008: dt: 0.0500, sse=20170454.0, rms=26.095 (0.375%)
009: dt: 0.0500, sse=20028784.0, rms=26.000 (0.365%)
010: dt: 0.0500, sse=19890884.0, rms=25.907 (0.358%)
positioning took 1.0 minutes
mean border=46.4, 57828 (53089) missing vertices, mean dist 9.6 [0.2
(%0.0)->13.3 (%100.0))]
%24 local maxima, % 7 large gradients and %40 min vals, 4827 gradients
ignored
tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2,
l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500,
l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=21510736.0, rms=26.320
011: dt: 0.0500, sse=21370844.0, rms=26.231 (0.338%)
012: dt: 0.0500, sse=21233808.0, rms=26.144 (0.333%)
013: dt: 0.0500, sse=21098910.0, rms=26.057 (0.331%)
014: dt: 0.0500, sse=20965742.0, rms=25.972 (0.329%)
015: dt: 0.0500, sse=20834178.0, rms=25.887 (0.327%)
016: dt: 0.0500, sse=20703918.0, rms=25.802 (0.326%)
017: dt: 0.0500, sse=20575078.0, rms=25.719 (0.324%)
018: dt: 0.0500, sse=20447296.0, rms=25.635 (0.324%)
019: dt: 0.0500, sse=20320634.0, rms=25.553 (0.323%)
020: dt: 0.0500, sse=20195002.0, rms=25.470 (0.323%)
positioning took 1.1 minutes
mean border=46.3, 57994 (51335) missing vertices, mean dist 9.3 [0.1
(%0.0)->12.8 (%100.0))]
%24 local maxima, % 7 large gradients and %40 min vals, 4820 gradients
ignored
tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2,
l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500,
l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=20284860.0, rms=25.363
021: dt: 0.0500, sse=20159524.0, rms=25.281 (0.323%)
022: dt: 0.0500, sse=20035252.0, rms=25.199 (0.323%)
023: dt: 0.0500, sse=19911852.0, rms=25.118 (0.322%)
024: dt: 0.0500, sse=19789384.0, rms=25.037 (0.322%)
025: dt: 0.0500, sse=19667922.0, rms=24.957 (0.322%)
026: dt: 0.0500, sse=19547232.0, rms=24.877 (0.322%)
027: dt: 0.0500, sse=19427442.0, rms=24.797 (0.321%)
028: dt: 0.0500, sse=19308560.0, rms=24.717 (0.321%)
029: dt: 0.0500, sse=19190536.0, rms=24.638 (0.321%)
030: dt: 0.0500, sse=19073444.0, rms=24.559 (0.320%)
positioning took 1.2 minutes
mean border=46.3, 58182 (49681) missing vertices, mean dist 9.0 [0.1
(%0.1)->12.4 (%99.9))]
%24 local maxima, % 7 large gradients and %40 min vals, 4842 gradients
ignored
tol=1.0e-04, sigma=2.0, host=unkno, 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
000: dt: 0.0000, sse=19160218.0, rms=24.467
031: dt: 0.5000, sse=18407090.0, rms=23.957 (2.084%)
032: dt: 0.5000, sse=17688926.0, rms=23.460 (2.077%)
033: dt: 0.5000, sse=17006668.0, rms=22.976 (2.063%)
034: dt: 0.5000, sse=16360864.0, rms=22.507 (2.040%)
035: dt: 0.5000, sse=15751547.0, rms=22.055 (2.009%)
036: dt: 0.5000, sse=15177610.0, rms=21.620 (1.973%)
037: dt: 0.5000, sse=14637857.0, rms=21.201 (1.936%)
038: dt: 0.5000, sse=14127666.0, rms=20.797 (1.904%)
039: dt: 0.5000, sse=13644749.0, rms=20.407 (1.877%)
040: dt: 0.5000, sse=13185130.0, rms=20.028 (1.856%)
041: dt: 0.5000, sse=12746617.0, rms=19.660 (1.838%)
042: dt: 0.5000, sse=12325521.0, rms=19.300 (1.832%)
043: dt: 0.5000, sse=11921329.0, rms=18.948 (1.825%)
044: dt: 0.5000, sse=11532627.0, rms=18.603 (1.819%)
045: dt: 0.5000, sse=11158549.0, rms=18.265 (1.816%)
046: dt: 0.5000, sse=10795637.0, rms=17.932 (1.826%)
047: dt: 0.5000, sse=10442737.0, rms=17.601 (1.845%)
048: dt: 0.5000, sse=10097535.0, rms=17.271 (1.871%)
049: dt: 0.5000, sse=9762229.0, rms=16.945 (1.887%)
050: dt: 0.5000, sse=9437930.0, rms=16.624 (1.896%)
051: dt: 0.5000, sse=9120953.0, rms=16.304 (1.927%)
052: dt: 0.5000, sse=8813598.0, rms=15.987 (1.940%)
053: dt: 0.5000, sse=8514504.0, rms=15.673 (1.965%)
054: dt: 0.5000, sse=8222812.0, rms=15.361 (1.991%)
055: dt: 0.5000, sse=7938257.0, rms=15.051 (2.021%)
056: dt: 0.5000, sse=7662795.0, rms=14.744 (2.040%)
Segmentation fault (core dumped)
Data were here:
https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i
------------------------
Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22>
Mon, 24 Feb 2020 06:34:51 -0800
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20200224>
Try setting -max XXX
where XXX is the maximum allowable thickness. It is default to 5, so
try something large
On 2/21/2020 11:36 AM, CiRong Liu wrote:
External Email - Use Caution
Dear experts of the freesurfer,
I was trying to create the white matter and pial surfaces of
the cerebellum of the marmoset, based on ultra-high (80um)
resolution ex-vivo images.I manually segment the cerebellum into
the white matter and the gray matter and change the header
information to 1mm.Based on the manual segmented files, I created
white matter surfaces (rh.orig).I tried to use the
mris_make_surfaces to expand the white matter to create the
matched pial surface.However, the /mris_make_surfaces/ failed to
push the surface enough. See the attached files and screenshots.I
tried smoothing the segmentation, enhancing the contrasts, and
tested different expert option (for example: -max_csf 0.1
-min_gray_at_csf_border 1)This was this best I got, but still
cannot get an optimal result (not pushed
enough):/mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1
-orig_wm orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm
marmosetceb rh /Since I have already manually segmented the
cerebellum, *is there a way to force the /mris_make_surfaces/ to
expand to the boundary of the image?*
The files can be download to replicate what I did:
https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i
Thank you very much!
Best Regards, CiRong Liu
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_____________________________________
Best Regards, CiRong Liu
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