External Email - Use Caution        

Hi Andrew

Thanks very much for this. I was able to patch the recon-all version in 7.1.0, not 7.1.1.  When I tried it with 7.1.1 I received a "permission denied" to "mv recon-all recon-all.backup".

I then re-ran recon-all -autorecon1, -autorecon2, and -autorecon3 in 7.1.0.  There was a Talairach error in autorecon1 and a few other errors in -autorecon2, and an "Unidentified variable" message at the end of -autorecon3.

When I run the $QA_TOOLS/recon_checker for this participant I get a long list of "ERROR .... missing output file" (and these output files are actually missing), as well as some commands and other outputs not found.

I"ve attached a zip file with the recon-all log.file, the recon_checker.log, a list of the errors I picked out of the recon-all.log, and the terminal output of the recon_checker that has a bit more info than the log file itself.

It seems there's still some significant problems--I hope you can guide me to a solution (e.g. perhaps remove 7.1.0 and reinstall 7.1.1?)

Cheers
James





On Fri, Sep 11, 2020 at 7:04 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Thanks for reporting this James. This is a bug in recon-all 7.1.1 that will be fixed in the next patch release. In the meantime, you can patch your version of recon-all with:

 

cd $FREESURFER_HOME/bin

mv recon-all recon-all.backup

curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon-all > recon-all

chmod +x recon-all

 

Let me know if you still run into any issues.

 

Best

Andrew

 

From: James Hartzell <james.hartzell@gmail.com>
Date: Friday, September 4, 2020 at 2:10 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>, "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: Freesurfer Digest, Vol 199, Issue 7

 

        External Email - Use Caution        

HI Andrew

 

Thanks. I've run autorecon 1, 2, and 3 so far for this one participant.

There's an error in autorecon 1 but I see from older list discussion that it can be safely ignored.

Even though autorecon 2 claims to finish without error, the error I reported seemed likely significant and I thought probably it should not be ignored--perhaps I am mistaken.

I've attached a zip file with all the logs in the scripts folder.

 

Cheers

James

 

On Fri, Sep 4, 2020 at 6:01 PM <freesurfer-request@nmr.mgh.harvard.edu> wrote:

Send Freesurfer mailing list submissions to
        freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: autorecon2, error MRISreadCurvature: (Hoopes, Andrew)
   2. Re: recon-all error (Jie Zhao)
   3. Re: mri_cvs_register with sub-millimeter recons
      (Zollei, Lilla,Ph.D.)
   4. Re: recon-all error (Fischl, Bruce)
   5. mri_segstats quetsion (Nasiriavanaki, Zahra)


----------------------------------------------------------------------

Message: 1
Date: Thu, 3 Sep 2020 20:18:22 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] autorecon2, error MRISreadCurvature:
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <67B3E641-B123-4261-880B-BF3E194A8B87@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi James,

Can you send the full recon-all.log for this subject?

Thanks,
Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of James Hartzell <james.hartzell@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 3, 2020 at 10:20 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] autorecon2, error MRISreadCurvature:


        External Email - Use Caution
Hi

When running recon-all autorecon2, on a single subject with
(Macbook Pro 10.15.6 (19G2021), freesurfer-darwin-macOS-7.1.0-20200511-813297b)

it handles the rh.curv without a problem, but for the lh kicks out this error:

/Users...$subj.../surf
\n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm $subj lh curv sulc \n
             Toggling save flag on curvature files                       [ ok ]
                 Outputting results using filestem   [ ../stats/lh.curv.stats ]
             Toggling save flag on curvature files                       [ ok ]
                                   Setting surface [ $subj./lh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...error: No such file or directory
error: MRISreadCurvature: could not open /Users/$subj./surf/lh.curv

***WARNING!***
Some error has occurred while reading 'lh.curv'.
This might be due a vertex incompatibility
between the surface 'lh.smoothwm' and curv 'lh.curv'.

You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.

Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*************
Note /Users/$subj./surf/lh.curv does exist in the subject's surf folder.

I ran it twice just to be sure. I don't find an answer for the problem in the freesurfer list.  Any guidance will be much appreciated!
Cheers
James Hartzell, PhD (2x)
Donostia-San Sebati?n, Spain


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------------------------------

Message: 2
Date: Fri, 4 Sep 2020 16:21:06 +0800 (GMT+08:00)
From: "Jie Zhao" <zjuzhaojie@zju.edu.cn>
Subject: Re: [Freesurfer] recon-all error
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <6f0dbfa3.23119.17458347310.Coremail.zjuzhaojie@zju.edu.cn>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

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


> -----????-----
> ???: "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDU>
> ????: 2020-09-04 00:18:53 (???)
> ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> ??:
> ??: 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
> > >
> > >
> > >
> > > > -----????-----
> > > > ???: "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDU>
> > > > ????: 2020-08-27 23:39:20 (???)
> > > > ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> > > > ??:
> > > > ??: 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
> > > > >     >     
> > > > >     >     > -----????-----
> > > > >     >     > ???: "Tim Sch?fer" <ts+ml@rcmd.org>
> > > > >     >     > ????: 2020-08-23 16:24:28 (???)
> > > > >     >     > ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> > > > >     >     > ??:
> > > > >     >     > ??: 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 Sch?fer
> > > > >     >     >
> > > > >     >     > _______________________________________________
> > > > >     >     > 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



------------------------------

Message: 3
Date: Fri, 4 Sep 2020 12:17:31 +0000
From: "Zollei, Lilla,Ph.D." <LZOLLEI@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_cvs_register with sub-millimeter recons
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM6PR04MB44126E82C34D6B2B7EE4A2E3E32D0@DM6PR04MB4412.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="us-ascii"

Hi Noriana,
Do you have the log file from the cvs_registration itself? I assume that the recon for your data was successful.
Best, Lilla
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Noriana Jakopin <nejakopin1@gmail.com>
Sent: Thursday, September 3, 2020 1:45 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_cvs_register with sub-millimeter recons


        External Email - Use Caution

Hello Freesurfer Experts,
I have been trying to run mri_cvs_register to bring sub-millimeter data into MNI space, however the final outputs have large deformations to the brain. I have tried with both 0.5 mm and 0.7 mm using their respective sub-milimeter recons. It seems that the issue arises during Step 3(i) as the el_reg_tocvs_avg35_inMNI152.mgz does not have the deformations, but the step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz file does. Does anyone have any guidance on how I can troubleshoot this?

I have attached the recon-all.log file for the 0.7 mm data. If you need me to share any other files, let me know.

FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1
Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS

Thank you,
Noriana Jakopin
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Message: 4
Date: Fri, 4 Sep 2020 14:27:48 +0000
From: "Fischl, Bruce" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BL0PR04MB66094CEE4F4A215DF49162A5EF2D0@BL0PR04MB6609.namprd04.prod.outlook.com>

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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


> -----????-----
> ???: "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDU>
> ????: 2020-09-04 00:18:53 (???)
> ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> ??:
> ??: 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
> > >
> > >
> > >
> > > > -----????-----
> > > > ???: "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDU>
> > > > ????: 2020-08-27 23:39:20 (???)
> > > > ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> > > > ??:
> > > > ??: 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
> > > > >     >     
> > > > >     >     > -----????-----
> > > > >     >     > ???: "Tim Sch?fer" <ts+ml@rcmd.org>
> > > > >     >     > ????: 2020-08-23 16:24:28 (???)
> > > > >     >     > ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> > > > >     >     > ??:
> > > > >     >     > ??: 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 Sch?fer
> > > > >     >     >
> > > > >     >     > _______________________________________________
> > > > >     >     > 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
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> >
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>
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Message: 5
Date: Fri, 4 Sep 2020 15:56:02 +0000
From: "Nasiriavanaki, Zahra" <ZNASIRIAVANAKI@mgh.harvard.edu>
Subject: [Freesurfer] mri_segstats quetsion
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <DF4C2760-46E5-4E62-8D6F-DF79745AAFB6@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Dear Freesurferers

Hi

I am trying to extract the BOLD signal values from a functional subcortical area. I did the below steps to make the functional thalamus ROI and then used the mri_segstats to extract the BOLD signal from it.
I would like to know 1-if my approach is correct? 2- should I use ?lhthal3? as a mask? if so, what should I use as an input? 3-I see that the ?mri_segstats? outputs one value for each voxel inside my ROI, is there a way to get one value across the whole ROI (lhthal3.nii.gz)?

fslmaths 'aseg.nii.gz' -thr 10 -uthr 10 'lhthal.nii.gz'
fslmaths 'lhthal.nii.gz' -mul 'sig.nii.gz' 'lhthal2.nii.gz'
fslmaths 'lhthal2.nii.gz' -bin 'lhthal3.nii.gz'

mri_segstats --seg aseg.nii.gz --i lhthal3.nii.gz  --sfavg this.txt

Thanks a lot
M0na

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

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End of Freesurfer Digest, Vol 199, Issue 7
******************************************



--

James Hartzell, PhD (2x)

Donostia-San Sebatián, Spain

Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy

Center for Buddhist Studies, Columbia University, USA

 

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.


--
James Hartzell, PhD (2x)
Donostia-San Sebatián, Spain
Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy
Center for Buddhist Studies, Columbia University, USA