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Hello Freesurfer Team
I am trying to segment the macaque brain. After skull strip,
control point adding and white matter editing, I try to inflate the
brain surface.
My command is :recon-all -s monkey2
-autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80
The output error is:
#@# WhitePreAparc lh 2020年 10月 05日 星期一 13:23:44 CST
cd /usr/local/freesurfer/subjects/monkey2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5
7.1.0
7.1.0
cd /usr/local/freesurfer/subjects/monkey2/mri
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5
Reading in input surface ../surf/lh.orig
Smoothing surface with 5 iterations
Area 230166 0.28728 0.06614 0.000899 0.5852
Corner 690498 60.00000 9.22592 3.263084 157.1301
Edge 345249 0.81774 0.11586 0.028436 1.5900
Hinge 345249 4.79409 6.13323 0.000002 153.5438
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=30761, wmmin=5, clip=110
MRIfindBrightNonWM(): 6937 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
ERROR: need seg for ripping
Command exited with non-zero status 1
@#@FSTIME 2020:10:05:13:23:44 mris_place_surface N 14 e 12.39 S 0.16 U 10.80 P 88% M 434260 F 25 R 126035 W 0 c 3134 w 27 I 5168 O 0 L 1.41 1.59 1.40
@#@FSLOADPOST 2020:10:05:13:23:56 mris_place_surface N 14 1.32 1.56 1.39
Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Can you help me explain above error and how to
solve this problem?
I have attached the wm.mgz,but recon-all.log and brainmask.mgz are beyond the size limit . Thanks in advance!
All best,
Jie