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

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

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

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-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

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" 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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach Registration,but some error occured in the tkregister, so some button were not functioning well.

I can not find useful info. on the internet, could you tell me how to correct it.Thanks.

Please check the error log file attached.

King regards, Jie

-----Original Messages----- From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU Sent Time: 2020-08-28 00:06:31 (Friday) To: freesurfer@nmr.mgh.harvard.edu Cc: Subject: Re: [Freesurfer] recon-all error

This is the automatic failure detection raising a warning flag. Did you notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

...

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-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

     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" 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

---

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

External Email - Use Caution

tkregister2 --s mprage --fstal , below is the error:

Determinant 26.9764

subject = mprage Zoom Factor = 2, SQR() = 4 FOV = 256 Opening window mprage Opening mprage, xnum = 256, xdim = 512 Setting scale Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4

This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary" tkregister2: interface: /usr/local/freesurfer/tktools/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} % invalid command name "tk::ScreenChanged" while executing "tk::ScreenChanged :0.0" (changing screen in event binding)

-----Original Messages----- From:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU Sent Time:2020-08-29 23:31:44 (Saturday) To: freesurfer@nmr.mgh.harvard.edu Cc: Subject: Re: [Freesurfer] recon-all error

What is the error? tkregister2 is an old program, and it might not work on all systems. You can try using tkregisterfv instead, available here https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv

On 8/29/2020 11:26 AM, Jie Zhao wrote:

External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach Registration,but some error occured in the tkregister, so some button were not functioning well.

I can not find useful info. on the internet, could you tell me how to correct it.Thanks.

Please check the error log file attached.

King regards, Jie

-----Original Messages----- From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU Sent Time: 2020-08-28 00:06:31 (Friday) To: freesurfer@nmr.mgh.harvard.edu Cc: Subject: Re: [Freesurfer] recon-all error

This is the automatic failure detection raising a warning flag. Did you notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

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-bounces@nmr.mgh.harvard.edufreesurfer-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

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" 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Try running it with --no-surfs

On 8/29/20 12:34 PM, Jie Zhao wrote:

External Email - Use Caution

Hi, Douglas

I first heared the tkregisterfv, tryed the tkregisterfv --fstal --s mprage

the output error was this:

ERROR: cannot find /usr/local/freesurfer/subjects/mprage/surf/lh.white

Best,

Jie

-----Original Messages-----
*From:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
*Sent Time:*2020-08-29 23:31:44 (Saturday)
*To:* freesurfer@nmr.mgh.harvard.edu
*Cc:*
*Subject:* Re: [Freesurfer] recon-all error

What is the error? tkregister2 is an old program, and it might not
work on all systems. You can try using tkregisterfv instead,
available here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv

On 8/29/2020 11:26 AM, Jie Zhao wrote:

...

         External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach Registration,but some error occured in the tkregister, so some button were not  functioning well.

I can not find useful info. on the internet, could you tell me how to correct it.Thanks.

Please check the error log file attached.

King regards,
Jie

...

-----Original Messages-----
From: "Douglas N. Greve"<dgreve@MGH.HARVARD.EDU>  Sent Time: 2020-08-28 00:06:31 (Friday)
To:freesurfer@nmr.mgh.harvard.edu  Cc:
Subject: Re: [Freesurfer] recon-all error

This is the automatic failure detection raising a warning flag. Did you
notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

...

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-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

          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"<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  _______________________________________________
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  

_______________________________________________
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  

_______________________________________________
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  

_______________________________________________
Freesurfer mailing listFreesurfer@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

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

    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" 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

---

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

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

    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" 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

---

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

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

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" 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

---

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

Hi Jie,

Is this a scan of a non-human primate?

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@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-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

    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" 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

---

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

Oh. Talairach is a human atlas - you won't be able to register a macaque to it

Sorry Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Jie Zhao Sent: Friday, September 4, 2020 4:21 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Yes , It is the macaque subject from Siemens 7T MRI

-----原始邮件----- 发件人: "Fischl, Bruce" BFISCHL@MGH.HARVARD.EDU 发送时间: 2020-09-04 00:18:53 (星期五) 收件人: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] recon-all error

Hi Jie,

Is this a scan of a non-human primate?

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@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-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

    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" 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

---

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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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

This is  not something we do. I have seen it done before, so do a search online and/or talk to the authros

On 9/6/2020 11:43 PM, Jie Zhao wrote:

     External Email - Use Caution

Hi, Bruce and all

The paper attached quoted "A semiautomated process was implemented to convert FreeSurfer generated macaque surfaces into Caret file formats and to register the individual hemispheres to the F99 atlas." Is the freesurfer have the function to generate macaque surface and how make it ?

Best, Jie

...

-----原始邮件----- 发件人: "Fischl, Bruce" BFISCHL@MGH.HARVARD.EDU 发送时间: 2020-09-04 22:27:48 (星期五) 收件人: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] recon-all error

Oh. Talairach is a human atlas - you won't be able to register a macaque to it

Sorry Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Jie Zhao Sent: Friday, September 4, 2020 4:21 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error

     External Email - Use Caution

Yes , It is the macaque subject from Siemens 7T MRI

...

-----原始邮件----- 发件人: "Fischl, Bruce" BFISCHL@MGH.HARVARD.EDU 发送时间: 2020-09-04 00:18:53 (星期五) 收件人: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] recon-all error

Hi Jie,

Is this a scan of a non-human primate?

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@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-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

     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" 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 > > > > _______________________________________________ > 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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