Hi Jie,
Is this a scan of a non-human primate?
Cheers
Bruce
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao
Sent: Thursday, September 3, 2020 9:34 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Hi, Bruce
I reorineted the views in freesurfer , But the result was wrong again . Please
check the figure attached, Is there any problem.
BTW, I got the Dicom file, it is .IMA format. How can I use it?
Thanks!
Jie
> -----Original Messages-----
> From: "Fischl, Bruce" <bfis...@mgh.harvard.edu> Sent Time: 2020-08-30
> 10:14:46 (Sunday)
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Cc:
> Subject: Re: [Freesurfer] recon-all error
>
> 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
> >
> > _______________________________________________
> > 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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