-----原始邮件-----
发件人: "Fischl, Bruce" <bfis...@mgh.harvard.edu>
发送时间: 2020-08-27 23:39:20 (星期四)
收件人: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
抄送:
主题: Re: [Freesurfer] recon-all error
Hi Jie
I would start by looking at your input volume in freeview, my
orientation on freeview is RAS. Could you tell me
freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
and make sure that the orientation it displays in is correct (that
is, that what freeview thinks is anterior/superior/left are indeed
those directions). Usually when we see this type of failure it is
because the direction cosines in the input volume are incorrect
(typically because the volume was at some point converted to
analyze format). Not always, but usually.
Cheers
Bruce
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao
Sent: Thursday, August 27, 2020 11:21 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Hi, Andrew
Attached is the right recon-all.log file, please check it.
I am new to the freesurfer, so really need you advice, Thanks
Kind Regards,
Jie
-----Original Messages-----
From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> Sent Time:
2020-08-26
10:17:00 (Wednesday)
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Cc:
Subject: Re: [Freesurfer] recon-all error
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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