Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary
Sorry, I don't know what else to tell you. On 2/28/2020 9:59 AM, CiRong Liu wrote: 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 0.00 nfields 0 scale 0.00 desired_rms_height 0.00 momentum 0.00 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., 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
Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary
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 0.00 nfields 0 scale 0.00 desired_rms_height 0.00 momentum 0.00 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., 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
Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
