The subject name when I call tksurfer, the subject name when I call tkmedit, and the subject name in the registration file are all exactly the same: red_badger. One thing I noticed is that in the left hemisphere everything seems normal (the activation is in the expected location); things only look weird in the right hemisphere. There's no possibility that the surface reconstruction could have been off the mark? Though it seems implausible that it would take the IPS and somehow warp it all the way onto the medial surface of the brain... 

Here are pictures of both the volume and surface views of the activation in question (it's the medial patch on the surface view, the patch with the red cursor in the volume view), in case they didn't load before for some reason. 

​​​​https://ibb.co/b8HFCv
https://ibb.co/cWYcQF

On Thu, Jul 6, 2017 at 12:00 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
        freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at
        freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: error message while using autorecon1 (Hoopes, Andrew)
   2. Re: error message while using autorecon1 (Buckless, Colleen)
   3. Re: Additional surface area (Bruce Fischl)
   4. Fwd: remove skull from gtmseg.mgz (miracle ozzoude)
   5. Re: error message while using autorecon1 (Hoopes, Andrew)
   6. Re: error message while using autorecon1 (Buckless, Colleen)
   7. Re: error message while using autorecon1 (Hoopes, Andrew)
   8. Re: recon-all on newborn (Lilla Zollei)
   9. Re: recon-all on newborn (Das S.)
  10. Re: Still confused by group analysis.. (Douglas Greve)
  11. Re: Raw Cortical thickness values (Douglas Greve)
  12. Re: Average myelination within ROI (Douglas Greve)
  13. Re: bbregister vs spmregister vs mri_coreg (Douglas Greve)
  14. Re: Recon-all: too many ('s (Douglas Greve)
  15. Re: Using multimodal slab input for hippocampus subfield
      segmentation in FS6 (Douglas Greve)
  16. Re: Strange Discrepancy Between Activation Location on
      Surface vs. Volume (Douglas Greve)
  17. Re: negative header after preproc-sess (Douglas Greve)
  18. Re: freesurfer@nmr.mgh.harvard.edu (Douglas Greve)
  19. Re: Building your own fsaverage (Douglas Greve)
  20. Re: Qdec error in analysis (Douglas Greve)
  21. Re: mri_glmfit error (mri_reshape number of elements)
      (Douglas Greve)
  22. Re: Fwd: remove skull from gtmseg.mgz (Douglas Greve)
  23. Re: GLM fitting for the cortical volume (Douglas Greve)
  24. Re: Subject with missing fMRI data (Douglas Greve)
  25. Re: Question mri_glmfit fwhm smoothing (Douglas Greve)
  26. Re: viewing mri_glmfit FDR corrected results (Douglas Greve)
  27. Re: content of "subjects_dir" (Douglas Greve)
  28. Re: Qdec error in analysis (AYUSHI SHUKLA)
  29. asegstats2table error (Elizabeth Dao)
  30. Re: Fwd: remove skull from gtmseg.mgz (miracooloz@gmail.com)


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

Message: 1
Date: Wed, 5 Jul 2017 17:29:23 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] error message while using autorecon1
To: "'freesurfer@nmr.mgh.harvard.edu'"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="Windows-1252"

Hi Colleen,
If you source freesurfer, and run:
ls $FREESURFER_HOME/mni/bin
It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced.
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 12:18 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] error message while using autorecon1

Hi All,
I am using the newest version of freesurfer, and I keep getting errors when I run recon-all ?autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log.
Any suggestions on how to fix this?
Thanks,

Colleen Buckless
Research Assistant
Center for Neurodevelopmental and Imaging Research
Kennedy Krieger Institute
443-923-2747
Buckless@kennedykrieger.org

________________________________
Disclaimer:


The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.



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

Message: 2
Date: Wed, 5 Jul 2017 17:36:47 +0000
From: "Buckless, Colleen" <Buckless@kennedykrieger.org>
Subject: Re: [Freesurfer] error message while using autorecon1
To: "'freesurfer@nmr.mgh.harvard.edu'"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org>
Content-Type: text/plain; charset="us-ascii"

Hi Andrew,
The output list includes nu_correct.
Thanks,
Colleen

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew
Sent: Wednesday, July 05, 2017 1:29 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

Hi Colleen,
If you source freesurfer, and run:
ls $FREESURFER_HOME/mni/bin
It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced.
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 12:18 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] error message while using autorecon1

Hi All,
I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log.
Any suggestions on how to fix this?
Thanks,

Colleen Buckless
Research Assistant
Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute
443-923-2747
Buckless@kennedykrieger.org

________________________________
Disclaimer:


The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=UD2JCpQKfeuIMEp7GIFvqrqCmqKkKCIa1NWotZOyhaY&e=


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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e=  . 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.




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

Message: 3
Date: Wed, 5 Jul 2017 13:51:41 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Additional surface area
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Michael

you need to look in the volume to see what is causing it. I would guess
some dura that is being incorrectly included, but you will be able to tell
in the slice view

cheers
Bruce


  On Mon, 3 Jul
2017, Michael Davies wrote:

>
> Hello, when inspecting a subject i discovered an anomaly on top of the 3D
> surface i have not previously encountered on other subjects i have
> inspected. Could you please let me know if this would be problematic when at
> the analysing group data please?
>
>
> Kind regards, Michael
>
>
>


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

Message: 4
Date: Wed, 5 Jul 2017 13:53:57 -0400
From: miracle ozzoude <miracooloz@gmail.com>
Subject: [Freesurfer] Fwd: remove skull from gtmseg.mgz
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CANfOk0h=UyBU_4ZV0E9mEaoE0NMvvx1_A-x63JxaLxj=54nuLg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

---------- Forwarded message ----------
From: miracle ozzoude <miracooloz@gmail.com>
Date: Tue, Jul 4, 2017 at 10:23 AM
Subject: remove skull from gtmseg.mgz
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>


Hello Freesurfer,

After running the first step of PETsurfer (https://surfer.nmr.mgh.
harvard.edu/fswiki/PetSurfer). I viewed the image it created using
freeview. When I change, the color map to Lookup Table, the image also
included the skull. How can I remove the skull from gtmseg.mgz/prevent it
from showing? Any help will be appreciated. Thanks. Please, see attached
image

Best,
Paul
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/93b99299/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gtmseg.mgz with skull.PNG
Type: image/png
Size: 42759 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/93b99299/attachment-0001.png

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

Message: 5
Date: Wed, 5 Jul 2017 18:04:52 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] error message while using autorecon1
To: "'freesurfer@nmr.mgh.harvard.edu'"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR04MB46620D3AC23D67DB97DDFA1F9D40@BLUPR04MB466.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

After sourcing freesurfer, what comes up if you run the command "which nu_correct"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS?
Thanks,
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 1:36 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

Hi Andrew,
The output list includes nu_correct.
Thanks,
Colleen

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew
Sent: Wednesday, July 05, 2017 1:29 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

Hi Colleen,
If you source freesurfer, and run:
ls $FREESURFER_HOME/mni/bin
It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced.
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 12:18 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] error message while using autorecon1

Hi All,
I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log.
Any suggestions on how to fix this?
Thanks,

Colleen Buckless
Research Assistant
Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute
443-923-2747
Buckless@kennedykrieger.org

________________________________
Disclaimer:


The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=UD2JCpQKfeuIMEp7GIFvqrqCmqKkKCIa1NWotZOyhaY&e=


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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e=  . 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.


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



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

Message: 6
Date: Wed, 5 Jul 2017 18:30:25 +0000
From: "Buckless, Colleen" <Buckless@kennedykrieger.org>
Subject: Re: [Freesurfer] error message while using autorecon1
To: "'freesurfer@nmr.mgh.harvard.edu'"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6F20C54B58C269489AA5CC858A1F58AF95128F@GSP-MAIL1.kki.org>
Content-Type: text/plain; charset="us-ascii"

I ran "which nu_correct" and it says command not found. What do you mean by the methods used to sourced FS? I am using a linux computing cluster to run FS on. Is this what you mean?
Thanks,
Colleen

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew
Sent: Wednesday, July 05, 2017 2:05 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

After sourcing freesurfer, what comes up if you run the command "which nu_correct"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS?
Thanks,
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 1:36 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

Hi Andrew,
The output list includes nu_correct.
Thanks,
Colleen

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew
Sent: Wednesday, July 05, 2017 1:29 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

Hi Colleen,
If you source freesurfer, and run:
ls $FREESURFER_HOME/mni/bin
It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced.
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 12:18 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] error message while using autorecon1

Hi All,
I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log.
Any suggestions on how to fix this?
Thanks,

Colleen Buckless
Research Assistant
Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute
443-923-2747
Buckless@kennedykrieger.org

________________________________
Disclaimer:


The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=UD2JCpQKfeuIMEp7GIFvqrqCmqKkKCIa1NWotZOyhaY&e=


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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e=  . 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.


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=HubYHC3fF4Ode82khCCkNpq9waX-NjnB0BZ2GvCZdgI&s=aYjmkFpTQ71v-1L1boJWOotq4bKM1KT58_bZv0nyZBM&e=

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=HubYHC3fF4Ode82khCCkNpq9waX-NjnB0BZ2GvCZdgI&s=aYjmkFpTQ71v-1L1boJWOotq4bKM1KT58_bZv0nyZBM&e=


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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIBAg&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=HubYHC3fF4Ode82khCCkNpq9waX-NjnB0BZ2GvCZdgI&s=pLbKfxrqMmVNrcnWzF2rplHuHHCk4hXhCPa-DN0EcVk&e=  . 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.




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

Message: 7
Date: Wed, 5 Jul 2017 18:56:47 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] error message while using autorecon1
To: "'freesurfer@nmr.mgh.harvard.edu'"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR04MB46640A60CF162E9923B0A95F9D40@BLUPR04MB466.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Sourcing FS is something you need to do before running any freesurfer programs in a new shell (terminal). The steps to do this are described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration

The standard method (when using csh) involves running:
setenv FREESURFER_HOME /usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

which will set some environment variables and make all FS commands available to you. Sourcing FS like this should fix your issue with nu_correct, if not, this could be a bug.

best,
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 2:30 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

I ran "which nu_correct" and it says command not found. What do you mean by the methods used to sourced FS? I am using a linux computing cluster to run FS on. Is this what you mean?
Thanks,
Colleen

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew
Sent: Wednesday, July 05, 2017 2:05 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

After sourcing freesurfer, what comes up if you run the command "which nu_correct"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS?
Thanks,
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 1:36 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

Hi Andrew,
The output list includes nu_correct.
Thanks,
Colleen

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew
Sent: Wednesday, July 05, 2017 1:29 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] error message while using autorecon1

Hi Colleen,
If you source freesurfer, and run:
ls $FREESURFER_HOME/mni/bin
It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced.
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org>
Sent: Wednesday, July 05, 2017 12:18 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] error message while using autorecon1

Hi All,
I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log.
Any suggestions on how to fix this?
Thanks,

Colleen Buckless
Research Assistant
Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute
443-923-2747
Buckless@kennedykrieger.org

________________________________
Disclaimer:


The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=UD2JCpQKfeuIMEp7GIFvqrqCmqKkKCIa1NWotZOyhaY&e=


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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e=  . 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.


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=HubYHC3fF4Ode82khCCkNpq9waX-NjnB0BZ2GvCZdgI&s=aYjmkFpTQ71v-1L1boJWOotq4bKM1KT58_bZv0nyZBM&e=

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=HubYHC3fF4Ode82khCCkNpq9waX-NjnB0BZ2GvCZdgI&s=aYjmkFpTQ71v-1L1boJWOotq4bKM1KT58_bZv0nyZBM&e=


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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIBAg&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=HubYHC3fF4Ode82khCCkNpq9waX-NjnB0BZ2GvCZdgI&s=pLbKfxrqMmVNrcnWzF2rplHuHHCk4hXhCPa-DN0EcVk&e=  . 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.


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



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

Message: 8
Date: Wed, 5 Jul 2017 17:32:27 -0400 (EDT)
From: Lilla Zollei <lzollei@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all on newborn
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1707042333040.8587@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; format=flowed; charset=US-ASCII


We use a similar pipeline but with different atlases and processing steps
for the newborns.
Lilla

On Wed, 5 Jul 2017, Das S. wrote:

>
> Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate.
>
> Autorecon Processing Stages:
>    Motion Correction and Conform
>    NU (Non-Uniform intensity normalization)
>    Talairach transform computation
>    Intensity Normalization 1
>    Skull Strip
>    EM Register (linear volumetric registration)
>    CA Intensity Normalization
>    CA Non-linear Volumetric Registration
>    Remove Neck
>    LTA with Skull
>    CA Label (Volumetric Labeling, ie Aseg) and Statistics
>    Intensity Normalization 2 (start here for control points)
>    White matter segmentation
>    Edit WM With ASeg
>    Fill (start here for wm edits)
>    Tessellation (begins per-hemisphere operations)
>    Smooth1
>    Inflate1
>    QSphere
>    Automatic Topology Fixer
>    Final Surfs (start here for brain edits for pial surf)
>    Smooth2
>    Inflate2
>    Spherical Mapping
>    Spherical Registration
>    Spherical Registration, Contralateral hemisphere
>    Map average curvature to subject
>    Cortical Parcellation - Desikan_Killiany and Christophe (Labeling)
>    Cortical Parcellation Statistics
>    Cortical Ribbon Mask
>    Cortical Parcellation mapping to Aseg
>
> BW
> S Das
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@nmr.mgh.harvard.edu]
> Sent: 04 July 2017 22:04
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all on newborn
>
> Hi S Das,
>
> We are trying to release the infant pipeline by the end of the summer.
>
> Lilla
>
> On Tue, 4 Jul 2017, Das S. wrote:
>
>> Dear Freesurfer expert,
>> I want to perform recon-all pipeline on neonates data.Can I do so?
>> I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all.
>> But again there is another paper where it says Freesurfer can perform segmentation of neonates image.
>> Any input will be appreciated.
>> Thanks
>> S Das
>>
>>
>> _______________________________________________
>> 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
>
>
> 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 Partners Compliance HelpLine at
> http://www.partners.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.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


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

Message: 9
Date: Wed, 5 Jul 2017 22:07:02 +0000
From: "Das S." <Sarbani.Das@soton.ac.uk>
Subject: Re: [Freesurfer] recon-all on newborn
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <97B5870E051A9548B7BAB625B7DC824A4D1DA030@SRV00047.soton.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Dear Lilla,
In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon.
If you give me little more details will be easy for me to understand the gap.
many thanks
Sarbani
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@nmr.mgh.harvard.edu]
Sent: 05 July 2017 22:32
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all on newborn

We use a similar pipeline but with different atlases and processing steps
for the newborns.
Lilla

On Wed, 5 Jul 2017, Das S. wrote:

>
> Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate.
>
> Autorecon Processing Stages:
>    Motion Correction and Conform
>    NU (Non-Uniform intensity normalization)
>    Talairach transform computation
>    Intensity Normalization 1
>    Skull Strip
>    EM Register (linear volumetric registration)
>    CA Intensity Normalization
>    CA Non-linear Volumetric Registration
>    Remove Neck
>    LTA with Skull
>    CA Label (Volumetric Labeling, ie Aseg) and Statistics
>    Intensity Normalization 2 (start here for control points)
>    White matter segmentation
>    Edit WM With ASeg
>    Fill (start here for wm edits)
>    Tessellation (begins per-hemisphere operations)
>    Smooth1
>    Inflate1
>    QSphere
>    Automatic Topology Fixer
>    Final Surfs (start here for brain edits for pial surf)
>    Smooth2
>    Inflate2
>    Spherical Mapping
>    Spherical Registration
>    Spherical Registration, Contralateral hemisphere
>    Map average curvature to subject
>    Cortical Parcellation - Desikan_Killiany and Christophe (Labeling)
>    Cortical Parcellation Statistics
>    Cortical Ribbon Mask
>    Cortical Parcellation mapping to Aseg
>
> BW
> S Das
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@nmr.mgh.harvard.edu]
> Sent: 04 July 2017 22:04
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all on newborn
>
> Hi S Das,
>
> We are trying to release the infant pipeline by the end of the summer.
>
> Lilla
>
> On Tue, 4 Jul 2017, Das S. wrote:
>
>> Dear Freesurfer expert,
>> I want to perform recon-all pipeline on neonates data.Can I do so?
>> I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all.
>> But again there is another paper where it says Freesurfer can perform segmentation of neonates image.
>> Any input will be appreciated.
>> Thanks
>> S Das
>>
>>
>> _______________________________________________
>> 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
>
>
> 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 Partners Compliance HelpLine at
> http://www.partners.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.
>
>
> _______________________________________________
> 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: 10
Date: Wed, 12 Jun 2013 22:22:59 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Still confused by group analysis..
To: Tudor Popescu <tudor3@gmail.com>,   free surfer
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <51B92D03.6050905@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


On 6/12/13 7:03 AM, Tudor Popescu wrote:
>
> Sorry Doug, wasn't sure whether you'd seen my last reply to this..
>
> On 6 Jun 2013 21:37, "Tudor Popescu" <tudor3@gmail.com
> <mailto:tudor3@gmail.com>> wrote:
>
>     Thanks Doug,
>
>
>
>             So if I want to use the study-specific "average" subject
>             surface with mri_surf2surf, rather than the generic
>             "fsaverage" one, how can this be done given that the
>             required ls.white file only exists in the latter but not
>             in the former? Can I just rename (or duplicate) ls.white
>             into ls.white_avg?
>
>         You can copy it or create a symbolic link.
>
>     So it is OK to copy the required lh.white file from the generic
>     average subject "fsaverage" and apply mri_surf2surf upon the
>     study-specific average subject ("average")? It still seems to me
>     that "average" should have its own (different) lh.white...
>
Yes it should. Did make_average_subject not create it?
>
>
>
>             Shouldn't the input to mri_glmfit be the output of
>             mri_surf2surf? In the group tutorial, the former is
>             "lh.gender_age.thickness.10.mgh" while the latter is
>             "lh.gender_age.thickness.10B.mgh". Or should it just be
>             the unsmoothed output of mris_preproc?
>
>         Yes, I can't remember why I put the "B" there, maybe to keep
>         people from overwriting  lh.gender_age.thickness.10.mgh during
>         the tutorial and having to wait the 10min or so for it to get
>         recreated.
>
>     But if all these commands transform the same file (output of
>     mris_preproc becomes input of mri_surf2surf, which then feeds into
>     mri_glmfit), then why is it still necessary to keep intact the
>     original lh.gender_age.thickness.10.mgh, when all you need for the
>     group analysis is the mri_surf2surf'd version?
>
Sorry, I'm lost here. What are the names of the files?
>
>
>
>             Assuming the label files (corresponding to my ROI, and
>             extracted from the Destrieux atlas) are different for each
>             subject, and given mri_glmfit is called just once, for all
>             subjects, which label file (corresponding to what subject)
>             should I point it to?
>
>         You need to create the label in the average subject. There is
>         a Destrieux atlas there.
>
>     Again, by "average subject" do you mean here the generic one
>     (fsaverage) or the study-specific one (average)? Should the former
>     be used at any point of a group analysis, if the latter exists?
>
If you are doing your group analysis on a custom average, then do not
use fsaverage at any point.
doug



-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130612/e5f65ff8/attachment.html

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

Message: 11
Date: Sun, 04 Aug 2013 13:34:56 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Raw Cortical thickness values
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <51FE90C0.1020701@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

They are in the ?h.thickness files. You can read them into matlab with
read_curv.m or you can convert them to nifti with mri_convert.
doug


On 8/5/13 5:28 AM, Muhammad Naveed Iqbal Qureshi wrote:
>
> Dear Community,
>
> I need to know how can I read the numeric cortical thickness values
> from freesurfer processed files. (as there are too many in the surf
> folder)
>
> Thank you.
>
> Best Regards
>
> Naveed
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130804/2875646c/attachment.html

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

Message: 12
Date: Wed, 03 Sep 2014 22:37:22 +0200
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Average myelination within ROI
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <54077C02.4060307@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


The min/max/etc are the voxel wise measures. When you use --accumulate,
it sums all the voxels but does not divide by the number of voxels, so
you get a number much larger than any one voxel
doug



On 9/3/14 9:44 PM, SHAHIN NASR wrote:
> Hi Surfers,
>
>     I want to measure the average amount of myelinations within my ROI(s),
>     I have already generated my myelination maps on surfaces (e.g.
> lh.myelin_ProjFrac0p5.nii ).  Then I used mri_segstats as below:
>
> mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1
> --sum V1_Stats.txt --accumulate
>
> but the numbers don't make any sense.  For instance:
>
> # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev
> Min Max Range
>   1   0    125261    82573.4  Seg0000 110280.4453 0.2922    -5.5000
> 51.0000    56.5000
>   2   1      1138      764.8  Seg0001   941.0988 0.1572     0.2675
> 1.4203     1.1527
>
> How can mean=941.0988 when the max=1.4203 ???
>
> Regards
> --
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140903/fa14be60/attachment.html

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

Message: 13
Date: Mon, 27 Feb 2017 10:55:29 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister vs spmregister vs mri_coreg
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <344aba48-650c-3286-a3e5-94afde4dd1ac@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

there is not an mri_spmregister (there is spmregister). If you have an
FA map, then I would use bbregister


On 2/25/17 8:03 PM, John Anderson wrote:
> Hi Doug, thank you for the detailed response. Highly appreciated!
> Kindly. I want to register FA map to structural T1 image using the
> command mri_spmregister as follow:
>
> mri_spmregister move FA.nii --s subj1 --reg reg dat --o FA_2_T1.nii.gz
>
> Is this correct?
>
>
>
>
>
>> -------- Original Message --------
>> Subject: bbregister vs spmregister vs mri_coreg
>> Local Time: February 25, 2017 8:49 AM
>> UTC Time: February 25, 2017 1:49 PM
>> From: John.anderso@protonmail.com
>> To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>
>> mri_coreg is the FS implementation of spm_coreg (spmregister) both of
>> which use normalized mutual info. bbregister uses the BBR cost
>> function and is preferred for all MRI. For registration to MNI space,
>> we usually use mni152reg (a wrapper around fsl's flirt)
>>
>>
>> On 2/25/17 8:49 AM, John Anderson wrote:
>>
>> Dear Freesurfer experts,
>>
>> I see that the tool "mri_coreg" has been implemented recently in Free
>> Surfer 6 and I really wanted to know what are the differences between
>> the registration tools "bbregister", " spmregister" and "mri_coreg"!
>> Kindly:
>>
>> 1. Are these tools similar? if not what are the differences ?
>>
>> 2. Is there any preference of using a tool over the others for
>> specific type of data. For example:
>>
>>          A. If I want to register FA map to T1 image which tool is
>> more robust?
>>
>>          B. if I want to register FA map to MNI space which tool is
>> more robust?
>>
>>
>>
>> I highly appreciate your input on this!
>>
>>
>> John t?e???Z??
>> Dear Freesurfer experts,
>> I see that the tool "mri_coreg" has been implemented recently in Free
>> Surfer 6 and I really wanted to know what are the differences between
>> the registration tools "bbregister", " spmregister" and "mri_coreg"!
>> Kindly:
>> 1. Are these tools similar? if not what are the differences ?
>> 2. Is there any preference of using a tool over the others for
>> specific type of data. For example:
>>            A. If I want to register FA map to T1 image which tool is
>> more robust?
>>            B. if I want to register FA map to MNI space which tool is
>> more robust?
>>
>>
>> I highly appreciate your input on this!
>>
>> John
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170227/bb174e10/attachment.html

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

Message: 14
Date: Wed, 5 Jul 2017 15:28:09 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all: too many ('s
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <172ef3dd-eea5-108f-f09e-b2fe813595c3@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Can you send the full log file?


On 7/3/17 4:03 AM, M del Mar Velasco wrote:
>
> Dear all,
>
> I am running a recon-all with
> Freesurfer-Linux-centos6_x86_64-dev-20170330-de24995 and Ubuntu 16.04:
>
>
>     recon-all -subjid subject_name -all
>
>
> I am using 0.65m3 images from RM. I get the message ' /Too many
> ('s/ '  and the recon-all stops at Aparc-to-Aseg. The recon.all.log
> doesn't state anything about this message. The analysis just stops. I
> have attached the log file and the screenshot about the message.
>
>
> Any idea about the reason about this issue? And how can I solve it?
>
>
> Thanks you in advance
>
>
> M del Mar
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/baf78081/attachment-0001.html

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

Message: 15
Date: Wed, 5 Jul 2017 15:31:28 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Using multimodal slab input for hippocampus
        subfield segmentation in FS6
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f383f9ef-1965-4972-53fa-56f6ac008878@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

What version of FS are you using? Can you send the recon-all.log file?


On 7/3/17 4:35 AM, Frauke Beyer wrote:
> Dear experts,
>
> I am trying to use T2-weighted images (0.5x0.5x1mm) as an additional
> scan to a T1-weighted image (0.7x0.7x0.7mm) for hippocampal subfield
> segmentation in Freesurfer 6. The T2-weighted data is a slab which
> includes the whole hippocampus and its y-axis is parallel to the
> hippocampal long axis (image dimensions [384,384,50]). When I try to use
> recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of
> additional scan> <analysisID>I always get a faulty alignment (through
> visual inspection by overlaying T2.FSspace.mgz on T1.mgz in freeview or
> by looking at the quality control image T1_to_T2.v10.QC.gif), even when
> I manually align the images beforehand.
>
> Do you have any idea or hint how to improve the registration and thus
> start the segmentation correctly? I also tried to find out which
> registration tool is used for this (mri_robust_register?) in order to
> play around with it and would also be thankful for any hint on this.
>
> Thank you for your advice and time,
>
> Best,
>
> Frauke
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>



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

Message: 16
Date: Wed, 5 Jul 2017 15:38:03 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Strange Discrepancy Between Activation
        Location on Surface vs. Volume
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <e947418e-78f3-c81f-e49a-b75b11a96bf6@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

So, it looks ok in the volume (using tkmedit) but not on the surface
(using tksurfer)? Something is definitely weird. The only thing I can
think of is that the surface is not the surface of the subject you think
it is. What is your tksurfer command line? What is the subject name in
the contents of the registration file?


On 7/3/17 11:39 AM, Taylor, Johnmark wrote:
> Hello,
>
> I am running into an odd issue. In particular, I have run a GLM
> analysis in _volume_ space, and I am visualizing the results both on
> the surface using tksurfer, and on the volume using tkmedit. In both
> cases, I am using the register.dof6.dat file to do the registration.
> Oddly, when I visualize the results on the _surface_, the activation
> patch falls on the medial surface of the hemisphere, in the
> _precuneus_, whereas when I visualize the results on the _volume_, the
> patch is in the _intraparietal sulcus_ (which is where we expect to
> see this particular activation). I have made a label out of the
> activation in both cases and viewed it in the other space just to make
> sure that it is in fact the same activation, and it is. Any idea what
> might be going on? It seems to me that it can't be an issue with the
> BOLD volume --> structural volume registration, since the activations
> look normal on tkmedit. It seems to me, then, that it must have to do
> with the relationship between the anatomical volume and the anatomical
> surface--could this be where the problem lies? Maybe an imperfect
> surface reconstruction?
>
> I've attached pictures of what I mean. The activation in question is
> in the right hemisphere. On the surface it can be seen on the medial
> part of the hemisphere , and in the volume it's where the red cursor
> is (as I mentioned, I verified by making labels that these are in fact
> the same activation).
>
> Thank you very much,
>
> JohnMark
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/de4d8a77/attachment-0001.html

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

Message: 17
Date: Wed, 5 Jul 2017 16:07:50 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] negative header after preproc-sess
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f2dba431-2464-0988-22af-f64cadc95776@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

When the nifti standard was adopted, they used a short int to represent
the dimensions. Unfortunately, this only allows for a maximum dimension
of 32k, which is not big enough for surfaces. So I hacked the FS nifti
format to put a -1 as the first dim at which point the FS code will go
to another place in the header to get the spatial dimensions. It is
possible to reshape the spatial dimensions as long as the largest prime
factor is less than 32k (see mri_surf2surf with --reshape option). Other
than that, you might ask the nibabel people to program the same hack.


On 6/25/17 6:48 AM, Bai Haohao wrote:
> Hello Freesurfer experts,
>
> I am running my data with preproc-sess to project my func data to
> individual anatomy file, and the command shows as below:
>
>     preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm
>     0 -per-run -force
>
>
> And the subjectname point to the subject dir that created after recon-all.
>
> After the running completed, I try to load data from
> fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:
>
>     >>> f.get_data()
>     Traceback (most recent call last):
>       File "<stdin>", line 1, in <module>
>       File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py",
>     line 341, in get_data
>         return np.asanyarray(self._data)
>       File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py",
>     line 512, in asanyarray
>         return array(a, dtype, copy=False, order=order, subok=True)
>       File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line
>     55, in __array__
>         self._data = self._read_data()
>       File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line
>     60, in _read_data
>         data = self.header.data_from_fileobj(fileobj)
>       File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line
>     486, in data_from_fileobj
>         data = self.raw_data_from_fileobj(fileobj)
>       File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line
>     458, in raw_data_from_fileobj
>         return array_from_file(shape, dtype, fileobj, offset)
>       File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line
>     493, in array_from_file
>         raise IOError(msg)
>     IOError: Expected -1804 bytes, got 264809160 bytes from file
>     "fmcpr.vol2surf.lh.nii.gz"
>      - could the file be damaged?
>
>
> Then I check the file header by nibabel, and I get this:
>
>
>     >>> print(f.get_header())
>     <class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
>     sizeof_hdr      : 348
>     data_type       :
>     db_name         :
>     extents         : 0
>     session_error   : 0
>     regular         :
>     dim_info        : 0
>     dim             : [  4  -1   1 1 451   1   1   1]
>     intent_p1       : 0.0
>     intent_p2       : 0.0
>     intent_p3       : 0.0
>     intent_code     : none
>     datatype        : float32
>     bitpix          : 32
>     slice_start     : 0
>     pixdim          : [-1.  1.          1.          1.
>      2.00000072  1.      1.
>       1.        ]
>     vox_offset      : 352.0
>     scl_slope       : 0.0
>     scl_inter       : 0.0
>     slice_end       : 0
>     slice_code      : unknown
>     xyzt_units      : 10
>     cal_max         : 0.0
>     cal_min         : 0.0
>     slice_duration  : 0.0
>     toffset         : 0.0
>     glmax           : 0
>     glmin           : 146790
>     descrip         : FreeSurfer May 13 2013
>     aux_file        :
>     qform_code      : scanner
>     sform_code      : scanner
>     quatern_b       : -0.0115927606821
>     quatern_c       : -0.996071338654
>     quatern_d       : -0.0864994972944
>     qoffset_x       : 73344.5546875
>     qoffset_y       : -1492.14978027
>     qoffset_z       : -2311.28955078
>     srow_x          : [ -9.99280393e-01   2.56918129e-02
>     2.79041883e-02 7.33445547e+04]
>     srow_y          : [  2.04970520e-02   9.84766901e-01
>      -1.72667429e-01  -1.49214978e+03]
>     srow_z          : [  3.19152586e-02   1.71971247e-01
>     9.84584868e-01  -2.31128955e+03]
>     intent_name     :
>     magic           : n+1
>
>
>
>
> Note that the dim has value -1, but when I use -surface fsaverage, the
> dim is correct(show as below):
>
>     dim       : [    4 27307     1     6   451     1     1     1]
>
>
> And I read the source code, the difference between self and fsaverage
> is appeared when running rawfunc2surf-sess, and log files are attached.
>
> I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz,
> such as fslview, freeview, mri_convert, mri_surf2surf, ...
>
> and only tksurfer could read this file by -timecourse
> fmcpr.sm0.self.lh.nii.gz.
>
> I want to figure out how could I fix it, and any suggestion would be
> helpful.
>
> Thanks in advance,
>
> Bai Haohao
>
>
> Version info:
> System: ubuntu-16.04.1-server-amd64
> Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
> nibabel: python-nibabel  1.2.2-1
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/bb7710c1/attachment-0001.html

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

Message: 18
Date: Wed, 5 Jul 2017 16:09:50 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9e4cf014-dd40-6599-ab44-f406739ba697@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

The orientation flag was not found. This is an important piece of
infomation that should be in the header. Have these dicoms been
anonymized? Alternatively, is this may be a newer version of dicom that
we are not reading properly yet.


On 6/25/17 9:45 PM, ?? wrote:
> Hi,
> I am preprocessing my fMRI data acquired with Philips. when I using
> the command 'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .....'
> The error occurred likes below:
> Found 31 total files.
> Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201
> Subject xxx
> Date xxx
> Time 110223
> Institution xxxxx.
> 0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002
> 101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003
> 301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004
> 401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007
> 501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008
> 601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011
> 701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013
> 801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016
> 901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018
> 1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019
> 1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022
> 1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024
> mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0
> nskip = 0
> ndrop = 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from ./XX_0003...
> Starting DICOMRead2()
> dcmfile = ./XX_0003
> dcmdir = .
> WARNING: tag image orientation not found in ./XX_0003
> Ref Series No = 101
> ERROR: bits = 0 not supported.
>
> My os is Linux 16.04 and the Freesurfer's version is 5.3.
>
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/79b9b6c8/attachment-0001.html

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

Message: 19
Date: Wed, 5 Jul 2017 16:12:03 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Building your own fsaverage
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b54957c4-bb6a-c3f6-de4e-ba1b6b58b0b5@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I have not looked at enough to really know. You may get a small boost in
power, but it will probably only help if the effects you are looking at
are right on the edge of significance.




On 6/26/17 1:26 AM, Silas wrote:
>
> Dear FreeSurfer team,
>
>
> I'm making a surface based group analysis of 40 multiple sclerosis
> subjects using FreeSurfer tools.
>
>
> What are the advantages of building your own
> fsaverage (make_average_subject) instead of using the premade
> fsaverage? Would you in general recommend this? What is the pro's and
> con's of building your own fsaverage?
>
>
> All the best,
>
> Silas
>
>
> I searched the mailing stream and found this answer:
>
> 'make_average_subject script, but as Doug implies you probably don't need to. Our warp is
> high-enough dimensional that you rarely need to build average subjects from
> your own population'
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/231bad1e/attachment-0001.html

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

Message: 20
Date: Wed, 5 Jul 2017 16:15:53 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Qdec error in analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <de7b3e56-fa55-f753-6eb9-4412efbaa886@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Do you have read permission to that file?


On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:
> Hi,
>
> I'm a new user of qdec and I'm trying to run a cortical thickness
> analysis in qdec between Schizophrenic patients and healthy controls.
> I have run "recon-all -i" and "recon-all -s <subjid> -qcache" on my
> data and it says that this has run successfully without any errors.
>
> But when I hit analyze on the qdec GUI, I get the following error-
>  "Error in Analyze: Couldn't open
> /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
> or .mgh file."
>
> I went through the old questions with the same issue, however I could
> not figure a solution for my problem as when I check in the directory,
> the file is present. I have tried to re-run recon-all and recon-all -s
> as well, but it is still giving the same error. I was wondering if
> someone could help me with this issue.
>
>
> Warm Regards
>
> Ayushi Shukla
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/dda913b4/attachment-0001.html

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

Message: 21
Date: Wed, 5 Jul 2017 16:24:32 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit error (mri_reshape number of
        elements)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <2eec8a7e-0615-7301-895a-d8d8800e3eb4@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

not sure what is going wrong. Does it work if you do not include the
--wls cesvar.nii.gz ?


On 6/28/17 12:29 PM, Mcnorgan, Christopher wrote:
> Hi,
> I?m running a group-level analysis and have encountered an error that
> results in a core dump. The first-level analyses were run using the
> fsaverage surfaces, rather than self surfaces. I?ve already inspected
> the individual contrasts, loading the fsaverage surface in tksurfer
> and rendering each subject?s contrast as an overlay, and would now
> like to compute the group-level results.
>
> I first ran isxconcat-sess, and saw no errors indicated in the program
> output.
>
> mri_glmfit was then called as followed, and produced the following
> output (same result for the rh):
>
>     $ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf
>     fsaverage lh --glmdir glm.wls --nii.gz
>     Reading source surface /home/chris/LDT/fsaverage/surf/lh.white
>     Number of vertices 163842
>     Number of faces  327680
>     Total area 65416.648438
>     AvgVtxArea 0.399267
>     AvgVtxDist 0.721953
>     StdVtxDist 0.195470
>
>     $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>     cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo
>     cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm
>     --surf fsaverage lh --glmdir glm.wls --nii.gz
>     sysname  Linux
>     hostname brocasarea
>     machine  x86_64
>     user     chris
>     FixVertexAreaFlag = 1
>     UseMaskWithSmoothing     1
>     OneSampleGroupMean 1
>     y  /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
>     logyflag 0
>     usedti  0
>     labelmask  /home/chris/LDT/fsaverage/label/lh.cortex.label
>     maskinv 0
>     glmdir glm.wls
>     IllCondOK 0
>     ReScaleX 1
>     DoFFx 0
>     wFile cesvar.nii.gz
>     weightinv  1
>     weightsqrt 1
>     Creating output directory glm.wls
>     Loading y from
>     /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
>     Saving design matrix to glm.wls/Xg.dat
>     Normalized matrix condition is 1
>     Matrix condition is 1
>     Found 149955 points in label.
>     ERROR: mri_reshape: number of elements cannot change
>       nv1 = 163842, nv1 = 537168
>     Pruning voxels by thr: 0.000000
>     Segmentation fault (core dumped)
>
>
> This seems to have its root in a mismatch between the vertices in the
> fsaverage lh.cortex label and those in the contrast data. However, I
> carried out subject-level analyses in the fsaverage surface space
> specifically to facilitate a group-level analysis in fsaverage surface
> space, so I can?t see where I went wrong. The only other post I could
> find that was similar was related to an attempt to carry out a group
> analysis in native surface space, which is not the case here.
>
> Thanks for your time
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/45f661a6/attachment-0001.html

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

Message: 22
Date: Wed, 5 Jul 2017 15:59:14 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: remove skull from gtmseg.mgz
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <2d72b1ad-926f-13d5-16ca-fbeae733265a@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You can change the color to be black or transparent.


On 7/5/17 10:53 AM, miracle ozzoude wrote:
>
> ---------- Forwarded message ----------
> From: *miracle ozzoude* <miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>>
> Date: Tue, Jul 4, 2017 at 10:23 AM
> Subject: remove skull from gtmseg.mgz
> To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>
>
> Hello Freesurfer,
>
> After running the first step of PETsurfer
> (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
> <https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer>). I viewed the
> image it created using freeview. When I change, the color map to
> Lookup Table, the image also included the skull. How can I remove the
> skull from gtmseg.mgz/prevent it from showing? Any help will be
> appreciated. Thanks. Please, see attached image
>
> Best,
> Paul
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/bbf43a1d/attachment-0001.html

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

Message: 23
Date: Wed, 5 Jul 2017 16:01:55 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] GLM fitting for the cortical volume
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <c5ec697b-2ccb-4b25-e109-358ad484a319@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

If you run mris_preproc, then specify --meas volume


On 6/24/17 3:10 PM, Ali Radaideh wrote:
> Dear FS experts,
>
> I have managed to run the *glm_fit* on the cortical thickness and area
> on a group of MS patients. However, i am not sure how to do this on
> the cortical volume. which file represents the cortical volume in
> subject's directory?
>
> Many thanks,
>
> --
> /Ali M. Al-Radaideh. PhD
> Head of Department of Medical Imaging
> Vice Dean of the Faculty of Allied Health Sciences
> The Hashemite University,
> Zarqa, Jordan
> W.phone +962 5 3903333 ext.5422, 5355, 5364
> Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>
> /
> /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/a228a6d8/attachment-0001.html

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

Message: 24
Date: Wed, 5 Jul 2017 16:28:55 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Subject with missing fMRI data
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <6c79411e-1f7e-6c7e-8ab7-857fe34c7a0e@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

We don't have any tools to do imputation. It is possible to have a
subject specific mask with the --frame-mask option to mri_glmfit. The
frame mask must be the same size as the input (--y) with 1s and 0s to
indicate whether a given voxel for a given subject should be included in
the model. I've not been happy with this method as it can create some
strange results as different voxels will now have different DOFs.


On 6/29/17 8:49 AM, Sadie Marvel wrote:
>
> Hi List,
>
>
> I am currently doing a group analysis of 26 subjects, one of which has
> missing fMRI data where the signal cuts off through parts of the
> occipital and temporal lobes. I was wondering if freesurfer has any
> way of dealing with this, such as multiple imputation, or other
> methods of filling the missing data. Alternatively, is there a way to
> only use the portions of the brain that have data when doing
> mri_glmfit? Does freesurfer do this automatically?
>
>
> Thanks.
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/b09930eb/attachment-0001.html

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

Message: 25
Date: Wed, 5 Jul 2017 17:39:03 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Question mri_glmfit fwhm smoothing
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <a8270423-76a3-e554-950f-6b84bd06ad4c@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

The fwhm.dat file contains the total amount of smoothness. The data have
inherent/endogenous smoothing and then you apply a certain amount, so
the total amount is different (more than) the amount you applied. To do
correction for multiple comparisons, mri_glmfit-sim needs to know how
smooth your data are (it needs the total smoothness). Smoothing by 25mm
is a lot I think. I usually use 5-10mm.



On 6/29/17 9:50 AM, Van Der Deijl, Rosanne wrote:
> Hi,
>
> I have a question about mri_glmfit. As an input, you give e.g. the
> stacked thickness data from all subjects, smoothed with a certain
> fwhm. But then as an output file, it gives an fwhm.dat file, which, at
> least in my case, contains another smoothing level.
>
> I noticed this because I ran mri_glmfit-sim forclusterwise multiple
> comparison correction, which gives me the error:
>
> ERROR: cannot find
> /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/rh/cortex/fwhm33/abs/th13/mc-z.csd
>
> As input I gave data smoothed to 25fwhm, and not fwhm33, as it seems
> to think. But indeed, in the fwhm.dat file it gives fwhm = 32.940499.
>
> I read in the tutorial that the fwhm.dat file contains the average
> FWHM of the residual.
> But still my questions are:
> - what this means
> - why mri_glmfit-sim would need this number, and whether/how I can run
> the mult. comparison correction on the 25fwhm-smoothed data.
>
> Thank you in advance!
>
> - Rose
>
> Commands:
> mri_glmfit:
> mri_glmfit --fsgd $CALMGREY/CALM_FSGD.txt dods --C
> CALMlong_contrast1.mat --C CALMlong_contrast2.mat --C
> CALMlong_contrast3.mat --C CALMlong_contrast4.mat --glmdir
> rh.CALMlong.thickness-spc.fwhm25 --y
> rh.CALMlong.thickness-spc.stack.fwhm25.mgh --cortex --surf fsaverage rh
>
> mri_glmfit-sim:
> mri_glmfit-sim --glmdir rh.CALMlong.thickness-spc.fwhm0 --cache 1.3
> neg --cwp --2spaces
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/efe06792/attachment-0001.html

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

Message: 26
Date: Wed, 5 Jul 2017 17:45:23 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing mri_glmfit FDR corrected results
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <fac83871-7cbd-68c2-fa5e-5bc2284e9fbc@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr
to the FDR you want. Set --subject fsaverage and set the ---hemi. Set
--annot aparc. Set --sum to the output summary file. This should give
you something similar to the output of mri_glmfit-sim.


On 6/29/17 4:29 PM, marco mcsweeney wrote:
> Dear FreeSurfer experts,
>
> I ran my group analysis using mri_glmfit and found a number of
> significant clusters showing cortical thickness differences between 2
> groups. I used tksurfer to visualize the results and used FDR to
> correct for multiple comparisons.
>
> My question is about how do I correctly get the FDR corrected results
> showing cluster number, size, MNI coordinates etc. as I would if I
> used QDEC?
>
> I have searched through the archives and have found what looks like
> the answer, but I'm not convinced that the method I used is correct.
>
> I used
>
> 1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs
> --cwpvalthresh .99
>
> and
>
> 2) less
> lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.cluster.summary
>
> However when I visualize the FDR corrected results with tksurfer or
> freeview I can see a couple of clusters not listed in the summary. Am
> I missing something?
>
> Thank you so much in advance.
>
> Any help or advice would be greatly appreciated.
>
> Best wishes
>
> Marco
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/ad6edb92/attachment-0001.html

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

Message: 27
Date: Wed, 5 Jul 2017 17:46:10 -0700
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] content of "subjects_dir"
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <19a7a69a-cb61-d0cc-3bf1-2cf2bff000db@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You don't need to move or copy anything. When you run recon-all, it will
automatically create a simlink to fsaverage.


On 6/29/17 9:04 PM, Schumman Resonance wrote:
> Dear free surfer community,
>
> Silly question here. I note the default "subjects_dir" in freesurfer
> contains a bunch of directories and files.
>
> If I set the environment so that my "subjects_dir" is not the default
> location, do I need to move any of the files in the original location
> to the new one?
>
> I hope this makes sense.
>
> Thanks,
>
> Kev
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170705/68ebb4e4/attachment-0001.html

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

Message: 28
Date: Thu, 06 Jul 2017 04:27:52 +0000
From: AYUSHI SHUKLA <ayushishukla@gmail.com>
Subject: Re: [Freesurfer] Qdec error in analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAGbhFQF8NPzPau0t90UvjkXq=+dz6ACfo_YO7TyNji65zKhX0A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi,

Thank you for your response.

Yes, I checked, and I do have the permission to read the file.

Warm Regards

Ayushi

On Thu, 6 Jul 2017 at 09:42, Douglas Greve <greve@nmr.mgh.harvard.edu>
wrote:

> Do you have read permission to that file?
>
> On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:
>
> Hi,
>
> I'm a new user of qdec and I'm trying to run a cortical thickness analysis
> in qdec between Schizophrenic patients and healthy controls.
> I have run "recon-all -i" and "recon-all -s <subjid> -qcache" on my data
> and it says that this has run successfully without any errors.
>
> But when I hit analyze on the qdec GUI, I get the following error-  "Error
> in Analyze: Couldn't open
> /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
> or .mgh file."
>
> I went through the old questions with the same issue, however I could not
> figure a solution for my problem as when I check in the directory, the file
> is present. I have tried to re-run recon-all and recon-all -s as well, but
> it is still giving the same error. I was wondering if someone could help me
> with this issue.
>
>
> Warm Regards
>
> Ayushi Shukla
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
>
>
> 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 Partners Compliance
> HelpLine at
> http://www.partners.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.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170706/2fb99810/attachment-0001.html

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

Message: 29
Date: Thu, 6 Jul 2017 00:33:27 -0700
From: Elizabeth Dao <elizabethdao@gmail.com>
Subject: [Freesurfer] asegstats2table error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CADa8Lt-y-gczx5k6Z7xhg2kGjktB_MUn+cA=2h31DdvVMGvETg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear experts,

I have completed recon-all with no errors. Now I would like to use the
'asegstats2table' command but I've received the error below. I would
appreciate any help in solving this problem. I am using FreeSurfer v6.0.0
on a Linux CentOS machine.

[TLA@CogmobCentOS MCI]$ asegstats2table --subjects 201.MR1 202.MR1 203.MR1
--meas volume --tablefile aseg_stats_all.txt
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line 4, in
<module>
    import os
  File "/usr/local/lib/python2.7/os.py", line 398, in <module>
    import UserDict
  File "/usr/local/lib/python2.7/UserDict.py", line 84, in <module>
    _abcoll.MutableMapping.register(IterableUserDict)
  File "/usr/local/lib/python2.7/abc.py", line 109, in register
    if issubclass(subclass, cls):
  File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__
    cls._abc_negative_cache.add(subclass)
  File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add
    self.data.add(ref(item, self._remove))
TypeError: cannot create weak reference to 'classobj' object

Thank you in advance for your help!

Liz
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170706/64cbbe40/attachment-0001.html

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

Message: 30
Date: Thu, 06 Jul 2017 08:46:15 -0400
From: miracooloz@gmail.com
Subject: Re: [Freesurfer] Fwd: remove skull from gtmseg.mgz
To: Douglas Greve <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <20170706124615.7307348.4410.4619@gmail.com>
Content-Type: text/plain; charset="us-ascii"

An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170706/40b90712/attachment-0001.html

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

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

End of Freesurfer Digest, Vol 161, Issue 13
*******************************************