Hi Jie
The orientations are incorrect. What freeview thinks is anterior/posterior
(labeled with "A" and "P") is actually inferior/superior. Do you have the
dicoms from this dataset? If not, how was it converted? You need to orient it
properly so it shows correctly in freeview before we will be able to process it.
Cheers
Bruce
-----
-----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 10:08 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Here is the snapshot of my freeview window attached.
> -----Original Messages-----
> From: "Fischl, Bruce" <bfis...@mgh.harvard.edu> Sent Time: 2020-08-30
> 02:07:50 (Sunday)
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Cc:
> Subject: Re: [Freesurfer] recon-all error
>
> 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
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
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>
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