Hi Jie, this appears to be the log for your original issue, and not the
talairach registration failure.
Andrew
On 8/25/20, 9:23 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie
Zhao" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
zjuzhao...@zju.edu.cn> wrote:
External Email - Use Caution
Hi Andrew
Thanks fro your response.
I have soruced the Freesurfer.
Attached is the recon-all log.
Best,
Jie
> -----Original Messages-----
> From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
> Sent Time: 2020-08-24 22:22:28 (Monday)
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Cc:
> Subject: Re: [Freesurfer] recon-all error
>
> Hi Jie,
>
> Can you send the subject's full recon-all.log file to provide some more
context for this failure? Usually this error is due to a poor registration, but
there might be something else going wrong here based on those p values. Have
you sourced freesurfer in your environment? Adding the freesurfer bin dir to
your PATH will provide access to binaries, but there are a few other PATH
variables and settings that get configured by running `source
$FREESURFER_HOME/SetUpFreeSurfer.sh`.
>
> best
> Andrew
>
> On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of Jie Zhao" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
zjuzhao...@zju.edu.cn> wrote:
>
> External Email - Use Caution
>
> Hi, Tim
>
> Thanks for your quick response.
> I set the PATH environment varible to include Freesurfer binary
directory.
>
> I have the new problem when using recon-all , the error is like this:
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050
>
> How can solve this error?
>
> Regards,
> Jie
>
> > -----原始邮件-----
> > 发件人: "Tim Schäfer" <ts...@rcmd.org>
> > 发送时间: 2020-08-23 16:24:28 (星期日)
> > 收件人: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> > 抄送:
> > 主题: Re: [Freesurfer] recon-all error
> >
> > External Email - Use Caution
> >
> > What happems if you type 'mri_ca_label' in your shell?
> >
> > Did you setup your PATH environment variable to include the
Freesurfer binary directory?
> >
> > Tim
> >
> > > On August 23, 2020 at 9:34 AM Jie Zhao <zjuzhao...@zju.edu.cn>
wrote:
> > >
> > >
> > > External Email - Use Caution
> > >
> > > Dear freesurfer developer:
> > >
> > > I am using Freesurfer 7.1.1 and encounter an error like this when
using recon-all :
> > >
> > > zhao@zhao-VirtualBox:~$ export
SUBJECTS_DIR=/usr/local/freesurfer/subjects
> > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz
-autorecon1
> > > Subject Stamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > Current Stamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > > Actual FREESURFER_HOME /usr/local/freesurfer
> > > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24
06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> > > Segmentation fault
> > > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing
from the distribution?'
> > >
> > > What can I do to fix this? Thanks
> > >
> > >
> > >
> > >
> > > Best regards
> > >
> > > Jie Zhao
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Tim Schäfer
> >
> > _______________________________________________
> > 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 mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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