You can use the Transform volume tool in FreeView, though it will be a pain if you have to do a bunch. Getting the original dicoms is a much better place to start.

On 9/1/20 9:13 AM, Ellen Ji wrote:

       External Email - Use Caution
Dear Bruce (and Jie),

I believe I am encountering the same problem as Jie - see the attached screenshot from freeview. I was given niftis for a cohort of subjects and some of them are sideways. Thus, this resulted in Talairach failure when performing recon-all and cannot simply be readjusted using tkregister2 as far as I know.

What is the easiest way to fix the orientation?

Many thanks for your help,

Ellen

On 8/30/2020 4:14 AM, Fischl, Bruce wrote:

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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" <BFISCHL@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-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@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" <BFISCHL@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-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@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

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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" <AHOOPES@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-bounces@nmr.mgh.harvard.edu on behalf of Jie Zhao" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zjuzhaojie@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" <AHOOPES@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 $FREESURFER_HOME/SetUpFreeSurfer.sh`.
     >
     > best
     > Andrew
     >
     > On 8/24/20, 10:12 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jie Zhao" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zjuzhaojie@zju.edu.cn> wrote:
     >
     >             External Email - Use Caution
     >
     >     Hi, Tim
     >
     >     Thanks for your quick response.
     >     I set the PATH environment varible to include Freesurfer binary directory.
     >
     >     I have the new problem when using recon-all , the error is like this:
     >     ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050
     >
     >     How can solve this error?
     >
     >     Regards,
     >     Jie
     >
     >     > -----原始邮件-----
     >     > 发件人: "Tim Schäfer" <ts+ml@rcmd.org>
     >     > 发送时间: 2020-08-23 16:24:28 (星期日)
     >     > 收件人: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
     >     > 抄送:
     >     > 主题: Re: [Freesurfer] recon-all error
     >     >
     >     >         External Email - Use Caution
     >     >
     >     > What happems if you type 'mri_ca_label' in your shell?
     >     >
     >     > Did you setup your PATH environment variable to include the Freesurfer binary directory?
     >     >
     >     > Tim
     >     >
     >     > > On August 23, 2020 at 9:34 AM Jie Zhao <zjuzhaojie@zju.edu.cn> wrote:
     >     > >
     >     > >
     >     > >         External Email - Use Caution
     >     > >
     >     > > Dear freesurfer developer:
     >     > >
     >     > > I am using Freesurfer 7.1.1 and encounter an error like this when using recon-all :
     >     > >
     >     > > zhao@zhao-VirtualBox:~$ 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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