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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:

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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

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