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Thanks for your reply, Douglas.
When I ran mri_annotation2label, the same error occured. I'm sure there is enough space on my disk.
I updated my Freesurfer to version 7.1.1, and other mistake happened. For example, the default annotlist in 'surfreg' does not includes DKTatlas, but 'make_average_surface' includes this atlas. Even though the difference would not infulence the results,  when I build my atlas followed the instruction  http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi , the programm would  interrupt since it cannot find the DKTatlas in subj/xhemi/label dir. This bug is easy to handle, but there were other errors I couldn't  solve.  
I finally changed Freesurfer to version 5.3 and successfully built my atlas without error occured. From my opinion now, FS5.3 may be a better choice to build atlas by Xhemi.
 
chenlz@mail.bnu.edu.cn
 
From: Douglas N. Greve
Date: 2021-04-19 10:17
To: freesurfer
Subject: Re: [Freesurfer] Building atlas by Xhemi: Segmentation fault (core dumped)
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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