External Email - Use Caution Not sure what is going wrong here. Try running mri_annotation2label --subject myatlas.i3 --hemi lh --outdir /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214 --annotation aparc.a2009s Does it segfault in the same way? Can you confirm that you are not running out of disk space?
On 4/15/2021 2:47 AM, Li-Zhen Chen wrote: > > External Email - Use Caution > > Hello Freesurfer Developer， > I'm building my own symmetric atlas by Xhemi, something is wrong at > the final step(Make final iteration) > Here is my code: > > make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg > --subjects sub_01 sub_02 --xhemi --lh > > When I ran this code, a problem emerged. Here is part of the log: > > mris_seg2annot --seg > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh > > --ctab > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab > > --s myatlas.i3 --hemi lh --o > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot > > $Id: mris_seg2annot.c,v 1.10 2014/11/15 00:07:19 greve Exp $ > cwd /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3 > cmdline mris_seg2annot --seg > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh > > --ctab > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab > > --s myatlas.i3 --hemi lh --o > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot > > > sysname Linux > hostname chenlz-HP-ZHAN-99-Pro-G2-Microtower-PC > machine x86_64 > user chenlz > subject myatlas.i3 > hemi lh > surfseg > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh > ctab > > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab > annotfile > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot > Reading surface seg > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh > Reading surface > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/surf/lh.white > Reading ctab > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab > Writing annot to > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot > > Annot2std-Run-Time-Sec 16 > annot2std Done > mri_annotation2label --subject myatlas.i3 --hemi lh --outdir > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214 > > --annotation aparc.a2009s > subject = myatlas.i3 > annotation = aparc.a2009s > hemi = lh > outdir = > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214 > surface = white > > Reading surface > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/surf/lh.white > Loading annotations from > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot > reading colortable from annotation file... > colortable with 11176 entries read (originally > /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab) > Segmentation fault (core dumped) > ERROR: make_average_surface > > I run Freesurfer 6.0 on Ubuntu 18.04. I've tried to rerun my script > several times but I can't figure this problem out. What could be the > possible reasons? Any answer will be appreciated! > > Kind regards, > Jewel > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1zDIrXUBDmGPXCaew9rHlg0vvnc5wfuxR81aSVG5jgkrOC80A7dFNL6Xij3IGt6u9X9z86Svr5neKmWcRJQs6cvr6PtbDN4a2FvnKHTQ_rcDDcuxFHeTPGorcquhSulsroEoeC-isdz3bcdMNzf0gMtt8igXGaBYAImVJGlek8i_viMsjDuL-3aYwH7BlLqdMao8GS0-BydjleaTCcXOfAKrZmSmveTJbqNxJndxUrHNRjYzyZioZou0owPntTkx7mp5_tMNCkKTW4LlGXEjL2A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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