Hi James,

My apologies, I was thinking you had 7.1.1 installed. In general, I'd recommend updating your distribution to 7.1.1 if you have the opportunity (no change in recon results from 7.1.0). To fix this new "CBVfindFirstPeakD1: Undefined variable" error in your 7.1.0 install, please run the following. By the way, that permission error you received is probably because freesurfer was installed under root. Try prefacing these cmds with `sudo` to make changes with root privileges.

cd $FREESURFER_HOME/etc/ mv recon-config.yaml recon-config.yaml.backup curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/distribution/... > recon-config.yaml

Looking through the recon-all.log you attached, I don't see any indication of the other issues you mention.

Once again, thanks for pointing this bug out! It will be patched in the 7.1.2 release. One more thing - I notice you are manually running the autorecon stages back-to-back. In case you didn't know, the -all recon-all flag will run all of these stages automatically.

best Andrew

From: James Hartzell james.hartzell@gmail.com Date: Tuesday, September 15, 2020 at 6:08 AM To: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Cc: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer Digest, Vol 199, Issue 7

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.edumailto: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... > recon-all chmod +x recon-all

Let me know if you still run into any issues.

Best Andrew

From: James Hartzell <james.hartzell@gmail.commailto:james.hartzell@gmail.com> Date: Friday, September 4, 2020 at 2:10 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "Hoopes, Andrew" <AHOOPES@mgh.harvard.edumailto: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.edumailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu

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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)

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Message: 1 Date: Thu, 3 Sep 2020 20:18:22 +0000 From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2, error MRISreadCurvature: To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <67B3E641-B123-4261-880B-BF3E194A8B87@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of James Hartzell <james.hartzell@gmail.commailto:james.hartzell@gmail.com> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 3, 2020 at 10:20 AM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto: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.cnmailto:zjuzhaojie@zju.edu.cn> Subject: Re: [Freesurfer] recon-all error To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <6f0dbfa3.23119.17458347310.Coremail.zjuzhaojie@zju.edu.cnmailto: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.EDUmailto:BFISCHL@MGH.HARVARD.EDU> ????: 2020-09-04 00:18:53 (???) ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Sent Time: 2020-08-30 10:14:46 (Sunday) To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Sent Time: 2020-08-30 02:07:50 (Sunday) To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.EDUmailto:BFISCHL@MGH.HARVARD.EDU> ????: 2020-08-27 23:39:20 (???) ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.EDUmailto:AHOOPES@MGH.HARVARD.EDU> Sent Time: 2020-08-26 10:17:00 (Wednesday) To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jie Zhao" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zjuzhaojie@zju.edu.cnmailto: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<mailto:AHOOPES@MGH.HARVARD.EDU>>
> Sent Time: 2020-08-24 22:22:28 (Monday)
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu<mailto: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 $FREESURFER_HOME/SetUpFreeSurfer.sh`.
>
> best
> Andrew
>
> On 8/24/20, 10:12 AM, "freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jie Zhao" <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of zjuzhaojie@zju.edu.cn<mailto:zjuzhaojie@zju.edu.cn>> wrote:
>
>             External Email - Use Caution
>
>     Hi, Tim
>
>     Thanks for your quick response.
>     I set the PATH environment varible to include Freesurfer binary directory.
>
>     I have the new problem when using recon-all , the error is like this:
>     ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050
>
>     How can solve this error?
>
>     Regards,
>     Jie
>
>     > -----????-----
>     > ???: "Tim Sch?fer" <ts+ml@rcmd.org<mailto:ts%2Bml@rcmd.org>>
>     > ????: 2020-08-23 16:24:28 (???)
>     > ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
>     > ??:
>     > ??: Re: [Freesurfer] recon-all error
>     >
>     >         External Email - Use Caution
>     >
>     > What happems if you type 'mri_ca_label' in your shell?
>     >
>     > Did you setup your PATH environment variable to include the Freesurfer binary directory?
>     >
>     > Tim
>     >
>     > > On August 23, 2020 at 9:34 AM Jie Zhao <zjuzhaojie@zju.edu.cn<mailto:zjuzhaojie@zju.edu.cn>> wrote:
>     > >
>     > >
>     > >         External Email - Use Caution
>     > >
>     > > Dear freesurfer developer:
>     > >
>     > > I am using Freesurfer 7.1.1 and encounter an error like this when using recon-all :
>     > >
>     > > zhao@zhao-VirtualBox:~$ 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<mailto: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<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>

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

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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Noriana Jakopin <nejakopin1@gmail.commailto:nejakopin1@gmail.com> Sent: Thursday, September 3, 2020 1:45 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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

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

Content-Type: text/plain; charset="utf-8"

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error

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

-----????----- ???: "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> ????: 2020-09-04 00:18:53 (???) ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error

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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.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Sent Time: 2020-08-30 10:14:46 (Sunday) To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error

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Here is the snapshot of my freeview window attached.

...

-----Original Messages----- From: "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Sent Time: 2020-08-30 02:07:50 (Sunday) To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error

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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.EDUmailto:BFISCHL@MGH.HARVARD.EDU> ????: 2020-08-27 23:39:20 (???) ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error

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Hi, Andrew

Attached is the right recon-all.log file, please check it. I am new to the freesurfer, so really need you advice, Thanks

Kind Regards, Jie

...

-----Original Messages----- From: "Hoopes, Andrew" <AHOOPES@MGH.HARVARD.EDUmailto:AHOOPES@MGH.HARVARD.EDU> Sent Time: 2020-08-26 10:17:00 (Wednesday) To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jie Zhao" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zjuzhaojie@zju.edu.cnmailto: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<mailto:AHOOPES@MGH.HARVARD.EDU>>
> Sent Time: 2020-08-24 22:22:28 (Monday)
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu<mailto: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 $FREESURFER_HOME/SetUpFreeSurfer.sh`.
>
> best
> Andrew
>
> On 8/24/20, 10:12 AM, "freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jie Zhao" <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of zjuzhaojie@zju.edu.cn<mailto:zjuzhaojie@zju.edu.cn>> wrote:
>
>             External Email - Use Caution
>
>     Hi, Tim
>
>     Thanks for your quick response.
>     I set the PATH environment varible to include Freesurfer binary directory.
>
>     I have the new problem when using recon-all , the error is like this:
>     ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050
>
>     How can solve this error?
>
>     Regards,
>     Jie
>
>     > -----????-----
>     > ???: "Tim Sch?fer" <ts+ml@rcmd.org<mailto:ts%2Bml@rcmd.org>>
>     > ????: 2020-08-23 16:24:28 (???)
>     > ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
>     > ??:
>     > ??: Re: [Freesurfer] recon-all error
>     >
>     >         External Email - Use Caution
>     >
>     > What happems if you type 'mri_ca_label' in your shell?
>     >
>     > Did you setup your PATH environment variable to include the Freesurfer binary directory?
>     >
>     > Tim
>     >
>     > > On August 23, 2020 at 9:34 AM Jie Zhao <zjuzhaojie@zju.edu.cn<mailto:zjuzhaojie@zju.edu.cn>> wrote:
>     > >
>     > >
>     > >         External Email - Use Caution
>     > >
>     > > Dear freesurfer developer:
>     > >
>     > > I am using Freesurfer 7.1.1 and encounter an error like this when using recon-all :
>     > >
>     > > zhao@zhao-VirtualBox:~$ 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<mailto: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<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>

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

Message: 5 Date: Fri, 4 Sep 2020 15:56:02 +0000 From: "Nasiriavanaki, Zahra" <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Subject: [Freesurfer] mri_segstats quetsion To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <DF4C2760-46E5-4E62-8D6F-DF79745AAFB6@mgh.harvard.edumailto: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