Hi Jie
I would start by looking at your input volume in freeview:
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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