Why do you want to change it? Can you post a snapshot from freeview so we can
make sure we are on the same page?
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 12:25 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Hi Bruce
Thank you for quick answer。
I tryrd the freeview -v /usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my
freeview orienatation is RAS. could you tell me how to change it from RAS to
(ASL)anterior/superior/left. Thanks
Best,
Jie
> -----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
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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