[Freesurfer] mri_convert segfault error

[Joshua Lee]

On  freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu
16.04 LTS
mri_convert is seg faulting


>>ls brain*
> brain.finalsurfs.mgz  brainmask.auto.mgz  brainmask.mgz  brain.mgz
>
> mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii
>
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading from ./brain.mgz...
> Segmentation fault (core dumped)
>

Any ideas?

Thanks

Joshua
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Re: [Freesurfer] mri_convert segfault error

[Joshua Lee]

Hi Doug,

Yes the quoted lines were output fromt her terminal.

ls -l brain.mgz
> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
>

I have many Tb of disk space. I can chmod 777 the files and still seg
faults.

Thanks
Josh



-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
530.747.3805

On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve 
wrote:

> Can you send the full terminal output? Or is that it? Do you have enough
> disc space or is it running out? what is the result of
> ls -l brain.mgz
>
>
>
> On 06/02/2016 03:07 PM, Joshua Lee wrote:
> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on
> > Ubuntu 16.04 LTS
> > mri_convert is seg faulting
> >
> >
> > >>ls brain*
> > brain.finalsurfs.mgz brainmask.auto.mgz  brainmask.mgz  brain.mgz
> >
> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii
> >
> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> > reading from ./brain.mgz...
> > Segmentation fault (core dumped)
> >
> >
> > Any ideas?
> >
> > Thanks
> >
> > Joshua
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
___
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_convert segfault error

[Joshua Lee]

I had replaced the user name in the output I posted to the listserv for
security reasons. I am not on a virtual machine. Fresh install on bare
metal.
ls -l ../

...
> drwxr-xr-x 13 myuser myuser  4096 Jun  2 11:50 mri
> ...
>
>
-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
530.747.3805

On Thu, Jun 2, 2016 at 12:25 PM, dgw  wrote:

> Is this a virtual machine? (The username seems odd...)
>
> What is the output of whoami?
>
> What is the output of ls -l ../?
>
> hth
> d
>
>
>
> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee  wrote:
> > Hi Doug,
> >
> > Yes the quoted lines were output fromt her terminal.
> >
> >> ls -l brain.mgz
> >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
> >
> >
> > I have many Tb of disk space. I can chmod 777 the files and still seg
> > faults.
> >
> > Thanks
> > Josh
> >
> >
> >
> > -
> > Joshua Lee, Ph.D.
> > Post-Doctoral Researcher
> > MIND Institute
> > University of California, Davis
> > 530.747.3805
> >
> > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu>
> > wrote:
> >>
> >> Can you send the full terminal output? Or is that it? Do you have enough
> >> disc space or is it running out? what is the result of
> >> ls -l brain.mgz
> >>
> >>
> >>
> >> On 06/02/2016 03:07 PM, Joshua Lee wrote:
> >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on
> >> > Ubuntu 16.04 LTS
> >> > mri_convert is seg faulting
> >> >
> >> >
> >> > >>ls brain*
> >> > brain.finalsurfs.mgz brainmask.auto.mgz  brainmask.mgz  brain.mgz
> >> >
> >> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o
> ./brain.nii
> >> >
> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> >> > reading from ./brain.mgz...
> >> > Segmentation fault (core dumped)
> >> >
> >> >
> >> > Any ideas?
> >> >
> >> > Thanks
> >> >
> >> > Joshua
> >> >
> >> >
> >> >
> >> > ___
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> gr...@nmr.mgh.harvard.edu
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>
> >> ___
> >> 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
> >
> >
> > 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
>
___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_convert segfault error

[Joshua Lee]

I do note that I can enter "freeview ./brain.mgz" and the image opens. Then
I can manuall save it as a .nii

-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
530.747.3805

On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee  wrote:

> I had replaced the user name in the output I posted to the listserv for
> security reasons. I am not on a virtual machine. Fresh install on bare
> metal.
> ls -l ../
>
> ...
>> drwxr-xr-x 13 myuser myuser  4096 Jun  2 11:50 mri
>> ...
>>
>>
> -
> Joshua Lee, Ph.D.
> Post-Doctoral Researcher
> MIND Institute
> University of California, Davis
> 530.747.3805
>
> On Thu, Jun 2, 2016 at 12:25 PM, dgw  wrote:
>
>> Is this a virtual machine? (The username seems odd...)
>>
>> What is the output of whoami?
>>
>> What is the output of ls -l ../?
>>
>> hth
>> d
>>
>>
>>
>> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee  wrote:
>> > Hi Doug,
>> >
>> > Yes the quoted lines were output fromt her terminal.
>> >
>> >> ls -l brain.mgz
>> >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
>> >
>> >
>> > I have many Tb of disk space. I can chmod 777 the files and still seg
>> > faults.
>> >
>> > Thanks
>> > Josh
>> >
>> >
>> >
>> > -
>> > Joshua Lee, Ph.D.
>> > Post-Doctoral Researcher
>> > MIND Institute
>> > University of California, Davis
>> > 530.747.3805
>> >
>> > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu>
>> > wrote:
>> >>
>> >> Can you send the full terminal output? Or is that it? Do you have
>> enough
>> >> disc space or is it running out? what is the result of
>> >> ls -l brain.mgz
>> >>
>> >>
>> >>
>> >> On 06/02/2016 03:07 PM, Joshua Lee wrote:
>> >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on
>> >> > Ubuntu 16.04 LTS
>> >> > mri_convert is seg faulting
>> >> >
>> >> >
>> >> > >>ls brain*
>> >> > brain.finalsurfs.mgz brainmask.auto.mgz  brainmask.mgz  brain.mgz
>> >> >
>> >> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o
>> ./brain.nii
>> >> >
>> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>> >> > reading from ./brain.mgz...
>> >> > Segmentation fault (core dumped)
>> >> >
>> >> >
>> >> > Any ideas?
>> >> >
>> >> > Thanks
>> >> >
>> >> > Joshua
>> >> >
>> >> >
>> >> >
>> >> > ___
>> >> > Freesurfer mailing list
>> >> > Freesurfer@nmr.mgh.harvard.edu
>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >> --
>> >> Douglas N. Greve, Ph.D.
>> >> MGH-NMR Center
>> >> gr...@nmr.mgh.harvard.edu
>> >> Phone Number: 617-724-2358
>> >> Fax: 617-726-7422
>> >>
>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> >> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >>
>> >> ___
>> >> 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.
>> >>
>> >
>> >
>> > _

Re: [Freesurfer] mri_convert segfault error

[Joshua Lee]

Perhaps something to do with

libcrypt-2.*.so ??

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html

-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
530.747.3805

On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee  wrote:

> I do note that I can enter "freeview ./brain.mgz" and the image opens.
> Then I can manuall save it as a .nii
>
> -
> Joshua Lee, Ph.D.
> Post-Doctoral Researcher
> MIND Institute
> University of California, Davis
> 530.747.3805
>
> On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee  wrote:
>
>> I had replaced the user name in the output I posted to the listserv for
>> security reasons. I am not on a virtual machine. Fresh install on bare
>> metal.
>> ls -l ../
>>
>> ...
>>> drwxr-xr-x 13 myuser myuser  4096 Jun  2 11:50 mri
>>> ...
>>>
>>>
>> -
>> Joshua Lee, Ph.D.
>> Post-Doctoral Researcher
>> MIND Institute
>> University of California, Davis
>> 530.747.3805
>>
>> On Thu, Jun 2, 2016 at 12:25 PM, dgw  wrote:
>>
>>> Is this a virtual machine? (The username seems odd...)
>>>
>>> What is the output of whoami?
>>>
>>> What is the output of ls -l ../?
>>>
>>> hth
>>> d
>>>
>>>
>>>
>>> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee  wrote:
>>> > Hi Doug,
>>> >
>>> > Yes the quoted lines were output fromt her terminal.
>>> >
>>> >> ls -l brain.mgz
>>> >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
>>> >
>>> >
>>> > I have many Tb of disk space. I can chmod 777 the files and still seg
>>> > faults.
>>> >
>>> > Thanks
>>> > Josh
>>> >
>>> >
>>> >
>>> > -
>>> > Joshua Lee, Ph.D.
>>> > Post-Doctoral Researcher
>>> > MIND Institute
>>> > University of California, Davis
>>> > 530.747.3805
>>> >
>>> > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu>
>>> > wrote:
>>> >>
>>> >> Can you send the full terminal output? Or is that it? Do you have
>>> enough
>>> >> disc space or is it running out? what is the result of
>>> >> ls -l brain.mgz
>>> >>
>>> >>
>>> >>
>>> >> On 06/02/2016 03:07 PM, Joshua Lee wrote:
>>> >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on
>>> >> > Ubuntu 16.04 LTS
>>> >> > mri_convert is seg faulting
>>> >> >
>>> >> >
>>> >> > >>ls brain*
>>> >> > brain.finalsurfs.mgz brainmask.auto.mgz  brainmask.mgz
>>> brain.mgz
>>> >> >
>>> >> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o
>>> ./brain.nii
>>> >> >
>>> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>>> >> > reading from ./brain.mgz...
>>> >> > Segmentation fault (core dumped)
>>> >> >
>>> >> >
>>> >> > Any ideas?
>>> >> >
>>> >> > Thanks
>>> >> >
>>> >> > Joshua
>>> >> >
>>> >> >
>>> >> >
>>> >> > ___
>>> >> > Freesurfer mailing list
>>> >> > Freesurfer@nmr.mgh.harvard.edu
>>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >>
>>> >> --
>>> >> Douglas N. Greve, Ph.D.
>>> >> MGH-NMR Center
>>> >> gr...@nmr.mgh.harvard.edu
>>> >> Phone Number: 617-724-2358
>>> >> Fax: 617-726-7422
>>> >>
>>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> >> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>> >>
>>> >> ___
>>> >> Freesurfer mailing list
>>> >> Freesurfer@nmr.mgh.harvar

Re: [Freesurfer] mri_convert segfault error

[Joshua Lee]

Unfortunately this does not seem to work.

locate libcrypt-2


*/lib/x86_64-linux-gnu/libcrypt-2.23.so
<http://libcrypt-2.23.so>/lib32/libcrypt-2.23.so <http://libcrypt-2.23.so>*

cp /lib/x86_64-linux-gnu/libcrypt-2.23.so $FREESURFER_HOME/lib/libcrypt.so.1

[verified it copied, and added to lib path to environment]

echo $LD_LIBRARY_PATH


*/home/myuser/Tools/freesurfer/lib:/usr/lib/fsl/5.0*

cd ~/data/APP_FreeSurfer/APP_longitudinal/100604-200/mri
ls brain.*

*brain.mgz*

mri_convert -i ./brain.mgz -o ./help.nii



*$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from
./brain.mgz...Segmentation fault (core dumped)*


-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
530.747.3805

On Thu, Jun 2, 2016 at 12:44 PM, dgw  wrote:

> If you must use 5.1 (I would recommend upgrading), then try what Zeke
> suggested there.
>
> You beat me to the email ;)
>
> hth
> d
>
>
> On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee  wrote:
> > Perhaps something to do with
> >
> > libcrypt-2.*.so ??
> >
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html
> >
> > -
> > Joshua Lee, Ph.D.
> > Post-Doctoral Researcher
> > MIND Institute
> > University of California, Davis
> > 530.747.3805
> >
> > On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee  wrote:
> >>
> >> I do note that I can enter "freeview ./brain.mgz" and the image opens.
> >> Then I can manuall save it as a .nii
> >>
> >> -
> >> Joshua Lee, Ph.D.
> >> Post-Doctoral Researcher
> >> MIND Institute
> >> University of California, Davis
> >> 530.747.3805
> >>
> >> On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee  wrote:
> >>>
> >>> I had replaced the user name in the output I posted to the listserv for
> >>> security reasons. I am not on a virtual machine. Fresh install on bare
> >>> metal.
> >>> ls -l ../
> >>>
> >>>> ...
> >>>> drwxr-xr-x 13 myuser myuser  4096 Jun  2 11:50 mri
> >>>> ...
> >>>>
> >>>
> >>> -
> >>> Joshua Lee, Ph.D.
> >>> Post-Doctoral Researcher
> >>> MIND Institute
> >>> University of California, Davis
> >>> 530.747.3805
> >>>
> >>> On Thu, Jun 2, 2016 at 12:25 PM, dgw  wrote:
> >>>>
> >>>> Is this a virtual machine? (The username seems odd...)
> >>>>
> >>>> What is the output of whoami?
> >>>>
> >>>> What is the output of ls -l ../?
> >>>>
> >>>> hth
> >>>> d
> >>>>
> >>>>
> >>>>
> >>>> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee 
> wrote:
> >>>> > Hi Doug,
> >>>> >
> >>>> > Yes the quoted lines were output fromt her terminal.
> >>>> >
> >>>> >> ls -l brain.mgz
> >>>> >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
> >>>> >
> >>>> >
> >>>> > I have many Tb of disk space. I can chmod 777 the files and still
> seg
> >>>> > faults.
> >>>> >
> >>>> > Thanks
> >>>> > Josh
> >>>> >
> >>>> >
> >>>> >
> >>>> > -
> >>>> > Joshua Lee, Ph.D.
> >>>> > Post-Doctoral Researcher
> >>>> > MIND Institute
> >>>> > University of California, Davis
> >>>> > 530.747.3805
> >>>> >
> >>>> > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve
> >>>> > 
> >>>> > wrote:
> >>>> >>
> >>>> >> Can you send the full terminal output? Or is that it? Do you have
> >>>> >> enough
> >>>> >> disc space or is it running out? what is the result of
> >>>> >> ls -l brain.mgz
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >> On 06/02/2016 03:07 PM, Joshua Lee wrote:
> >>>> >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on
> >>>> >> > Ubuntu 16.04 LTS
> >>>> >> > mri_convert is seg faulting
> >>>> >> >
> >>>> >> >
> >>>> >> >

Re: [Freesurfer] mri_convert segfault error

[Joshua Lee]

Maybe its because its not an older version of that file from Ubuntu 12.04.

All the data is processed on a different machine, but I then import it on
my local machine for running different kinds of analyses (e.g. qdec). Will
it matter if I use the latest FreeSurfer version with data processed on 5.1?

Josh

-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
530.747.3805

On Thu, Jun 2, 2016 at 1:13 PM, Joshua Lee  wrote:

> Unfortunately this does not seem to work.
>
> locate libcrypt-2
>
>
> */lib/x86_64-linux-gnu/libcrypt-2.23.so
> <http://libcrypt-2.23.so>/lib32/libcrypt-2.23.so <http://libcrypt-2.23.so>*
>
> cp /lib/x86_64-linux-gnu/libcrypt-2.23.so
> $FREESURFER_HOME/lib/libcrypt.so.1
>
> [verified it copied, and added to lib path to environment]
>
> echo $LD_LIBRARY_PATH
>
>
> */home/myuser/Tools/freesurfer/lib:/usr/lib/fsl/5.0*
>
> cd ~/data/APP_FreeSurfer/APP_longitudinal/100604-200/mri
> ls brain.*
>
> *brain.mgz*
>
> mri_convert -i ./brain.mgz -o ./help.nii
>
>
>
> *$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading
> from ./brain.mgz...Segmentation fault (core dumped)*
>
>
> -
> Joshua Lee, Ph.D.
> Post-Doctoral Researcher
> MIND Institute
> University of California, Davis
> 530.747.3805
>
> On Thu, Jun 2, 2016 at 12:44 PM, dgw  wrote:
>
>> If you must use 5.1 (I would recommend upgrading), then try what Zeke
>> suggested there.
>>
>> You beat me to the email ;)
>>
>> hth
>> d
>>
>>
>> On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee  wrote:
>> > Perhaps something to do with
>> >
>> > libcrypt-2.*.so ??
>> >
>> >
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html
>> >
>> > -
>> > Joshua Lee, Ph.D.
>> > Post-Doctoral Researcher
>> > MIND Institute
>> > University of California, Davis
>> > 530.747.3805
>> >
>> > On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee  wrote:
>> >>
>> >> I do note that I can enter "freeview ./brain.mgz" and the image opens.
>> >> Then I can manuall save it as a .nii
>> >>
>> >> -
>> >> Joshua Lee, Ph.D.
>> >> Post-Doctoral Researcher
>> >> MIND Institute
>> >> University of California, Davis
>> >> 530.747.3805
>> >>
>> >> On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee 
>> wrote:
>> >>>
>> >>> I had replaced the user name in the output I posted to the listserv
>> for
>> >>> security reasons. I am not on a virtual machine. Fresh install on bare
>> >>> metal.
>> >>> ls -l ../
>> >>>
>> >>>> ...
>> >>>> drwxr-xr-x 13 myuser myuser  4096 Jun  2 11:50 mri
>> >>>> ...
>> >>>>
>> >>>
>> >>> -
>> >>> Joshua Lee, Ph.D.
>> >>> Post-Doctoral Researcher
>> >>> MIND Institute
>> >>> University of California, Davis
>> >>> 530.747.3805
>> >>>
>> >>> On Thu, Jun 2, 2016 at 12:25 PM, dgw  wrote:
>> >>>>
>> >>>> Is this a virtual machine? (The username seems odd...)
>> >>>>
>> >>>> What is the output of whoami?
>> >>>>
>> >>>> What is the output of ls -l ../?
>> >>>>
>> >>>> hth
>> >>>> d
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee 
>> wrote:
>> >>>> > Hi Doug,
>> >>>> >
>> >>>> > Yes the quoted lines were output fromt her terminal.
>> >>>> >
>> >>>> >> ls -l brain.mgz
>> >>>> >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
>> >>>> >
>> >>>> >
>> >>>> > I have many Tb of disk space. I can chmod 777 the files and still
>> seg
>> >>>> > faults.
>> >>>> >
>> >>>> > Thanks
>> >>>> > Josh
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> > -
>> >>>> > Joshua Lee, Ph.D.
>> >>>> > Post-Doctoral Researcher
>> >>>> > MIND Institute
>> >>>&

Re: [Freesurfer] mri_convert segfault error

[Joshua Lee]

Installing the latest version of FreeSurfer has resolved this problem. So
as long as the post-processing tools are compatible with these data then I
should be fine.

Thanks.

Josh

-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
530.747.3805

On Thu, Jun 2, 2016 at 1:20 PM, Joshua Lee  wrote:

> Maybe its because its not an older version of that file from Ubuntu 12.04.
>
> All the data is processed on a different machine, but I then import it on
> my local machine for running different kinds of analyses (e.g. qdec). Will
> it matter if I use the latest FreeSurfer version with data processed on 5.1?
>
> Josh
>
> -
> Joshua Lee, Ph.D.
> Post-Doctoral Researcher
> MIND Institute
> University of California, Davis
> 530.747.3805
>
> On Thu, Jun 2, 2016 at 1:13 PM, Joshua Lee  wrote:
>
>> Unfortunately this does not seem to work.
>>
>> locate libcrypt-2
>>
>>
>> */lib/x86_64-linux-gnu/libcrypt-2.23.so
>> <http://libcrypt-2.23.so>/lib32/libcrypt-2.23.so <http://libcrypt-2.23.so>*
>>
>> cp /lib/x86_64-linux-gnu/libcrypt-2.23.so
>> $FREESURFER_HOME/lib/libcrypt.so.1
>>
>> [verified it copied, and added to lib path to environment]
>>
>> echo $LD_LIBRARY_PATH
>>
>>
>> */home/myuser/Tools/freesurfer/lib:/usr/lib/fsl/5.0*
>>
>> cd ~/data/APP_FreeSurfer/APP_longitudinal/100604-200/mri
>> ls brain.*
>>
>> *brain.mgz*
>>
>> mri_convert -i ./brain.mgz -o ./help.nii
>>
>>
>>
>> *$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading
>> from ./brain.mgz...Segmentation fault (core dumped)*
>>
>>
>> -
>> Joshua Lee, Ph.D.
>> Post-Doctoral Researcher
>> MIND Institute
>> University of California, Davis
>> 530.747.3805
>>
>> On Thu, Jun 2, 2016 at 12:44 PM, dgw  wrote:
>>
>>> If you must use 5.1 (I would recommend upgrading), then try what Zeke
>>> suggested there.
>>>
>>> You beat me to the email ;)
>>>
>>> hth
>>> d
>>>
>>>
>>> On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee  wrote:
>>> > Perhaps something to do with
>>> >
>>> > libcrypt-2.*.so ??
>>> >
>>> >
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html
>>> >
>>> > -
>>> > Joshua Lee, Ph.D.
>>> > Post-Doctoral Researcher
>>> > MIND Institute
>>> > University of California, Davis
>>> > 530.747.3805
>>> >
>>> > On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee 
>>> wrote:
>>> >>
>>> >> I do note that I can enter "freeview ./brain.mgz" and the image opens.
>>> >> Then I can manuall save it as a .nii
>>> >>
>>> >> -
>>> >> Joshua Lee, Ph.D.
>>> >> Post-Doctoral Researcher
>>> >> MIND Institute
>>> >> University of California, Davis
>>> >> 530.747.3805
>>> >>
>>> >> On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee 
>>> wrote:
>>> >>>
>>> >>> I had replaced the user name in the output I posted to the listserv
>>> for
>>> >>> security reasons. I am not on a virtual machine. Fresh install on
>>> bare
>>> >>> metal.
>>> >>> ls -l ../
>>> >>>
>>> >>>> ...
>>> >>>> drwxr-xr-x 13 myuser myuser  4096 Jun  2 11:50 mri
>>> >>>> ...
>>> >>>>
>>> >>>
>>> >>> -
>>> >>> Joshua Lee, Ph.D.
>>> >>> Post-Doctoral Researcher
>>> >>> MIND Institute
>>> >>> University of California, Davis
>>> >>> 530.747.3805
>>> >>>
>>> >>> On Thu, Jun 2, 2016 at 12:25 PM, dgw  wrote:
>>> >>>>
>>> >>>> Is this a virtual machine? (The username seems odd...)
>>> >>>>
>>> >>>> What is the output of whoami?
>>> >>>>
>>> >>>> What is the output of ls -l ../?
>>> >>>>
>>> >>>> hth
>>> >>>> d
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee 
>>> wrote:
>>> >>>> > Hi Doug,
>>>

[Freesurfer] qdec load error missing BLT

[Joshua Lee]

When loading qdec I get

can't find package BLT
FsgdfPlot::InitFsgdf:  Couldn't find fsgdfPlot.tcl

on Ubuntu with FreeSurfer5.3
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Re: [Freesurfer] qdec load error missing BLT

[Joshua Lee]

contents of

$FREESURFER_HOME/lib/tcl/

allisons_surfaces.tcl  offsetmovie.tcl  TclChartWindow.tcl
curv-flat.tcl  phasemovie.tcl   test_layers.tcl
curv-views.tcl polar-flat.tcl   test_ScubaFrame.tcl
dara_data.tcl  polar-views.tcl  test_ScubaLayers.tcl
dipmovie-flat.tcl  readenv.tcl  test_TclCommandManager.tcl
eccen-flat.tcl real-flat.tcltest_tkUtils.tcl
eccen-views.tclreal-views.tcl   test_ToglManager.tcl
fs-flat.tclsaveflat.tcl test_view.tcl
fsgdfPlot.tcl  saveviews.tcltkcon.tcl
fs-make.tclscuba_glut.tcl   twocond-flat.tcl
fs-views.tcl   scuba.tcltwocond-masked-views.tcl
histolabel.tcl setdefpatchview.tcl  twocond-views.tcl
mk-fieldsign.tcl   solmovie-flat.tclwrappers.tcl


-
Joshua Lee, Ph.D.
Post-Doctoral Researcher
MIND Institute
University of California, Davis
916-703-0360

On Thu, Jun 23, 2016 at 1:16 PM, Joshua Lee  wrote:

> When loading qdec I get
>
> can't find package BLT
> FsgdfPlot::InitFsgdf:  Couldn't find fsgdfPlot.tcl
>
> on Ubuntu with FreeSurfer5.3
>
>
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[Freesurfer] (no subject)

[Joshua Lee]

Hello,

I noticed that Freesurfer's latest release offers an expert option "added
-first_wm_peak flag to mris_make_surfaces, which may aid accurate more
white matter surfaces especially in heavily myelinated areas like visual
cortex on data that is higher res than 1mm. enable the flag via an
expert.opts file."

Are these expert options doing something similar to what was done in
Lüsebrink, Wollrab, Speck, 2013 in *NeuroImage*, in which they " conforms
the data to the minimum voxel size, which is equal in all directions if
data with an isotropic resolution is used"

Thanks

Joshua
-
Joshua Lee
Doctoral Candidate
Department of Psychology &
Center for Mind and Brain
University of California, Davis
530.747.3805
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Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

[Joshua Lee]

Hi Alan,

Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x
0.4 mm in-plane resolution). The thickness of a CA subfield typically range
between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter
resolutions. Further, subfield segmentation typically requires
high-contrast data to discern the internal boundaries formed by the stratum
radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced
on a 1.5 T magnet can achieve the necessary contrast. Last, and please
someone correct me if what I say is inaccurate, but doesn't the Van Leemput
method use statistical priors to apply label probabilities in reference to
a generated hippocampal surface? This would imply that the method assigns
label probabilities without reference to a subject's SLRM intensity
information. For volumetry, I am somewhat skeptical that a method that only
relies on a generated surface  would be sensitive to group x subfield
interactions; especially double dissociations in which overall volume/shape
of the hippocampus may be similar across groups. That the that was
generated from potentially low resolution, low contrast data cannot help
the matter. Some may disagree about this though and I'd be interested in
hearing what other people think about the matter. In general, I am quite
optimistic about automated methods to segment the subfields.

Joshua



-
Joshua K. Lee
Doctoral Candidate
Department of Psychology &
Center for Mind and Brain
University of California, Davis



On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis wrote:

> Hi Bruce and FreeSurfers:
>
> I have received a manuscript to review for possible publication. The
> authors have used the subfields algorithm on 1.5T scans and obtained a
> parcellation with values. They have drawn some major conclusions on the
> basis of the findings. My understanding is that this method can only be
> done on 3T. Is the 1.5T results valid?
>
> Please advice.
>
> thanks,
>
> Alan Francis
>
> ___
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>
>
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> 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.
>
>
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Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

[Joshua Lee]

Thanks for the clarification Eugenio. Would saying that it relies on shape
instead of surface be more accurate? I would like to understand better.
Also, it is good news that there are plans to model the SLRM.
Josh

-
Joshua Lee
Doctoral Candidate
Department of Psychology &
Center for Mind and Brain
University of California, Davis
530.747.3805


On Mon, Apr 28, 2014 at 12:18 AM, Eugenio Iglesias wrote:

> Dear all,
> the current module in FreeSurfer works with 1mm T1 data, by relying on
> strong shape priors. So, at this point, feeding the algorithm data from a
> 3T scanner or a 1.5T scanner is pretty much the same.
> Joshua, it is indeed inaccurate to say that the method relies on a
> generated hippocampal surface, but you are definitely right regarding the
> SLRM: it is not modeled at this point (we have a new version that models it
> coming out hopefully soon!).
> Cheers,
> /Eugenio
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Joshua Lee" 
> To: "Freesurfer support list" 
> Sent: Friday, April 25, 2014 2:10:29 AM
> Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla
>
>
>
>
> Hi Alan,
>
> Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x
> 0.4 mm in-plane resolution). The thickness of a CA subfield typically range
> between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter
> resolutions. Further, subfield segmentation typically requires
> high-contrast data to discern the internal boundaries formed by the stratum
> radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced
> on a 1.5 T magnet can achieve the necessary contrast. Last, and please
> someone correct me if what I say is inaccurate, but doesn't the Van Leemput
> method use statistical priors to apply label probabilities in reference to
> a generated hippocampal surface? This would imply that the method assigns
> label probabilities without reference to a subject's SLRM intensity
> information. For volumetry, I am somewhat skeptical that a method that only
> relies on a generated surface would be sensitive to group x subfield
> interactions; especially double dissociations in !
>  which overall volume/shape of the hippocampus may be similar across
> groups. That the that was generated from potentially low resolution, low
> contrast data cannot help the matter. Some may disagree about this though
> and I'd be interested in hearing what other people think about the matter.
> In general, I am quite optimistic about automated methods to segment the
> subfields.
>
>
>
>
> Joshua
>
>
>
>
>
>
>
> -
>
> Joshua K. Lee
> Doctoral Candidate
>
> Department of Psychology &
> Center for Mind and Brain University of California, Davis
>
>
>
>
> On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis < alandarkene...@gmail.com> 
> wrote:
>
>
>
> Hi Bruce and FreeSurfers:
>
> I have received a manuscript to review for possible publication. The
> authors have used the subfields algorithm on 1.5T scans and obtained a
> parcellation with values. They have drawn some major conclusions on the
> basis of the findings. My understanding is that this method can only be
> done on 3T. Is the 1.5T results valid?
>
> Please advice.
>
> thanks,
>
> Alan Francis
> ___
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
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>
>
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> e-mail
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> error
> but does not contain patient information, please contact the sender

[Freesurfer] advice in registering a binary mask to Freesurfer space.

[Joshua Lee]

Hi All,

I wanted to get peoples advice on the best method of
registration/interpolation to use on a manually traced segmentation (and
its structural) that is not in the same space and orientation as the
structurals I started Freesurfer with (although they both originally came
from the same image. I want to maintain the integrity of the manual traced
binary mask through this registration and reslice. For a number of reasons,
I do not want to take Freesurfers output to the space of the manual
segmentation.

What do people think is a good technique? Flirt nearest neighbor
interpolation? Something different from Freesurfer? ANTs?
-
Josh
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Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.

[Joshua Lee]

Hi Doug.
That was in fact what I decided to do.

Thanks!

Josh
-
J


On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve
wrote:

>
> Can you compute the registration between the manually traced anat space
> and the FS conformed space? Eg, with BBR. If you can do that, then you
> can run mri_label2vol to convert the mask into FS conformed space
> (assuming that that is what you want to do).
> doug
>
> On 03/22/2013 04:43 PM, Joshua Lee wrote:
> > Hi All,
> >
> > I wanted to get peoples advice on the best method of
> > registration/interpolation to use on a manually traced segmentation
> > (and its structural) that is not in the same space and orientation as
> > the structurals I started Freesurfer with (although they both
> > originally came from the same image. I want to maintain the integrity
> > of the manual traced binary mask through this registration and
> > reslice. For a number of reasons, I do not want to take Freesurfers
> > output to the space of the manual segmentation.
> >
> > What do people think is a good technique? Flirt nearest neighbor
> > interpolation? Something different from Freesurfer? ANTs?
> > -
> > Josh
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.

[Joshua Lee]

Hi Doug,

Is a standard 12 affine registration sufficient to get a subjects
structural (in a different orientation) into the same space as norm.mgz, or
will I need some non-linear registration? Basically, what kind of
transforms are applied to go from orig to norm?
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee  wrote:

> Hi Doug.
> That was in fact what I decided to do.
>
> Thanks!
>
> Josh
> -
> J
>
>
> On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Can you compute the registration between the manually traced anat space
>> and the FS conformed space? Eg, with BBR. If you can do that, then you
>> can run mri_label2vol to convert the mask into FS conformed space
>> (assuming that that is what you want to do).
>> doug
>>
>> On 03/22/2013 04:43 PM, Joshua Lee wrote:
>> > Hi All,
>> >
>> > I wanted to get peoples advice on the best method of
>> > registration/interpolation to use on a manually traced segmentation
>> > (and its structural) that is not in the same space and orientation as
>> > the structurals I started Freesurfer with (although they both
>> > originally came from the same image. I want to maintain the integrity
>> > of the manual traced binary mask through this registration and
>> > reslice. For a number of reasons, I do not want to take Freesurfers
>> > output to the space of the manual segmentation.
>> >
>> > What do people think is a good technique? Flirt nearest neighbor
>> > interpolation? Something different from Freesurfer? ANTs?
>> > -
>> > Josh
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.

[Joshua Lee]

I see. To clarify. orig is the conformed version of the original input
file, which means just sampling to 1 mm as needed, and cropping to 256
matrix. norm.mgz has some intensity corrections, but does not include
spatial changes.

I had read http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
and I thought that maybe that spatial warping was involved beyond
resampling to the original dimensions/resolution to get to  "native space".
This simplifies things greatly. Thank you both.


On Mon, Mar 25, 2013 at 1:56 PM, Bruce Fischl wrote:

> Hi Josh,
>
> there are no spatial transforms to go from orig to norm. They are in the
> same space.
>
> cheers
> Bruce
>
>
> On Mon, 25 Mar 2013, Joshua Lee wrote:
>
>  Hi Doug,
>>
>> Is a standard 12 affine registration sufficient to get a subjects
>> structural
>> (in a different orientation) into the same space as norm.mgz, or will I
>> need
>> some non-linear registration? Basically, what kind of transforms are
>> applied
>> to go from orig to norm?
>> -
>> Joshua Lee
>> Graduate Student
>> Center for Mind and Brain &
>> Department of Psychology
>> University of California, Davis
>> 530.747.3805
>>
>>
>> On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee  wrote:
>>   Hi Doug.
>>   That was in fact what I decided to do.
>>
>>   Thanks!
>>
>>   Josh
>>   -
>> J
>>
>>
>> On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve
>>  wrote:
>>
>>   Can you compute the registration between the manually
>>   traced anat space
>>   and the FS conformed space? Eg, with BBR. If you can do
>>   that, then you
>>   can run mri_label2vol to convert the mask into FS
>>   conformed space
>>   (assuming that that is what you want to do).
>>   doug
>>
>>   On 03/22/2013 04:43 PM, Joshua Lee wrote:
>>   > Hi All,
>>   >
>>   > I wanted to get peoples advice on the best method of
>>   > registration/interpolation to use on a manually traced
>>   segmentation
>>   > (and its structural) that is not in the same space and
>>   orientation as
>>   > the structurals I started Freesurfer with (although they
>>   both
>>   > originally came from the same image. I want to maintain
>>   the integrity
>>   > of the manual traced binary mask through this
>>   registration and
>>   > reslice. For a number of reasons, I do not want to take
>>   Freesurfers
>>   > output to the space of the manual segmentation.
>>   >
>>   > What do people think is a good technique? Flirt nearest
>>   neighbor
>>   > interpolation? Something different from Freesurfer?
>>   ANTs?
>>   > -
>>   > Josh
>>   >
>>   >
>> > __**_
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>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
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[Freesurfer] subcortical segmentation

[Joshua Lee]

A subcortical segmentation error sometimes get Freesurfer (v 5.1) is
cortical areas coming over into the hippocampus, ignoring the wm inferior
and lateral to the hippocmapus (coronal). See attached png.
Will adding wm control points help, or do they not inform the aseg
segmentation. What is the best way to (non-manually) fix this kind of issue?

-
Josh
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[Freesurfer] aseg.mgz altered after auto-recon2?

[Joshua Lee]

Hi All,

Am I right in reading the dev table that if I just want the aseg.mgz, (not
the stats output), I only need to run auto-recon1 and auto-recon2?

I need to run 250+ brains just to get the aseg volume, so if I can shave
off 4-10 hours off each that would be huge.
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Re: [Freesurfer] aseg.mgz altered after auto-recon2?

[Joshua Lee]

In fact, couldn't I stop after calabel if all I want is the aseg.mgz?
-
Josh


On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee  wrote:

> Hi All,
>
> Am I right in reading the dev table that if I just want the aseg.mgz, (not
> the stats output), I only need to run auto-recon1 and auto-recon2?
>
> I need to run 250+ brains just to get the aseg volume, so if I can shave
> off 4-10 hours off each that would be huge.
>
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Re: [Freesurfer] aseg.mgz altered after auto-recon2?

[Joshua Lee]

Hey thanks,

I haven't worried about multi threading typically since I just run more
brains simultaneously. On my computer, I have sufficient 64 gigs RAM (64
gigs) and 24 CPU/cores (not sure which)  to run 20 recon-all scripts
simultaneously at full speed. Would I still benefit from the multi
threading? I am a little confused about cores vs cpus

I created a copy of the recon-all script that stops at calabel step, and am
running that now.
-
Josh


On Thu, Mar 28, 2013 at 12:58 PM, Natalie Han  wrote:

> Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats
> if you don't want the statistics file (aseg.stats). Also, use -openmp 8 can
> speed up quite a lot by multi-threading. For a regular T1 brain image, I
> can the running time to get aseg.mgz in about 4-5 hours.
>
> recon-all -i subject autorecon1 -subcortseg -nosegstats -openmp 8
>
> cheers,
> Natalie
>
>
> On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl  > wrote:
>
>> Hi Josh,
>>
>> yes, I think that's correct.
>>
>> Bruce
>> On Thu, 28 Mar 2013, Joshua Lee wrote:
>>
>> > In fact, couldn't I stop after calabel if all I want is the aseg.mgz?
>> > -
>> > Josh
>> >
>> >
>> > On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee 
>> wrote:
>> >   Hi All,
>> >
>> >   Am I right in reading the dev table that if I just want the
>> >   aseg.mgz, (not the stats output), I only need to run auto-recon1
>> >   and auto-recon2?
>> >
>> >   I need to run 250+ brains just to get the aseg volume, so if I
>> >   can shave off 4-10 hours off each that would be huge.
>> >
>> >
>> >
>> >
>> ___
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[Freesurfer] advice for subcortical Freesurfer processing of 2 year old brains

[Joshua Lee]

The aseg has shown poor performance in my sample. Are there settings,
atlases, etc, available that might improve performance?
-
Josh
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Re: [Freesurfer] advice for subcortical Freesurfer processing of 2 year old brains

[Joshua Lee]

Looking forward to it.
-
Josh


On Tue, Apr 2, 2013 at 11:32 AM, Lilla Zollei
wrote:

>
> Hi Josh,
>
> We do not yet have a publicly available atlas for that population. We are
> working on it though and will announce it as soon as it is ready.
>
> Lilla
>
>
> On Tue, 2 Apr 2013, Joshua Lee wrote:
>
>  The aseg has shown poor performance in my sample. Are there settings,
>> atlases, etc, available that might improve performance?
>> -
>> Josh
>>
>>
>>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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[Freesurfer] failures more frequent in one hemisphere

[Joshua Lee]

Hi All,

I recently ran a number of  2-yr-old brains through Freesurfer, and overall
Freesurfer did well considering the age group. However, a subset (~10%) had
catastrophic failures in the left termporal lobe in which parahippocampal
cortex bled over into the hippocampal region. I've since added control
points and am rerunning. However, what I found curious was that almost
every failure was in the left hemisphere, not the right. Any ideas why that
might happen?

Using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

Joshua
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[Freesurfer] hipposubfields and data

[Joshua Lee]

I have read that the hippo-subfield algorithm uses the aseg for
initialization, and then uses the original MRI data. By original, does that
mean it up-samples the conformed 1mm data to .5mm, or does that mean it
takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and
upsamples it to .5mm?

Josh
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Re: [Freesurfer] hipposubfields and data

[Joshua Lee]

I think the resolution is important. The CA1 subfield is only about 2-2.5
mm thick after all.

If this is a feature request thread now, let me add that it would be nice
if the actual training algorithm was integrated into Freesurfer. There is a
lot of disagreement about the most appropriate subfield boundaries, and the
ability to make custom training sets would be helpful.

Right now there is little guidance on what kind of data-sets are
appropriate to use with this algorithm. I am concerned that users are
trying to segment subfields with older data-sets that probably aren't
appropriate (e.g. 1.5 Tesla or 1.5 mm isotropic data).


Josh


On Tue, May 28, 2013 at 1:44 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

> Hi Josh,
> as of now, it uses nu.mgz, which is conformed and bias field corrected
> with N3.
> Koen, do you think we should add a flag to change this? The algorithm is
> pretty resolution-independent, and could certainly benefit from
> higher-res data.
> Cheers,
> /Eugenio
>
> On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote:
> > I have read that the hippo-subfield algorithm uses the aseg for
> > initialization, and then uses the original MRI data. By original, does
> > that mean it up-samples the conformed 1mm data to .5mm, or does that
> > mean it takes the original original input (i.e. my 0.7 mm isotropic
> > MPRAGE) and upsamples it to .5mm?
> >
> > Josh
> > ___
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> --
> Juan Eugenio Iglesias, PhD
> http://www.jeiglesias.com
> igles...@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
>
>
>
>
>
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[Freesurfer] subfield algorithm and subject intensity differences

[Joshua Lee]

I'm trying to understand Leemput's subfield algorithm better as implemented
in Freesurfer. Does the algorithm make use of intensity differences in the
internal hippocampal lamina from the subject's T1 image to warp meshes and
assign subfield probabilities? Or does it depend only on outward boundaries
of the hippocampus and probability priors to determine the inner boundaries
between CAs and dentate gyrus?
-
Josh
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Re: [Freesurfer] subfield algorithm and subject intensity differences

[Joshua Lee]

Thanks Bruce and Eugenio,

 Suppose I had two identical images of a subject, but in one image I
reduced the contrast of internal lamina while leaving the rest of the image
intact...just removing internal intensity differences, but leaving the
outer boundary contrast intact.

Would the images result in very different subfield segmentations?

Josh


-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Fri, Jun 7, 2013 at 12:33 PM, Bruce Fischl wrote:

> Hi Josh
>
> it depends on intensity differences if it can find them as well as
> boundary/geometry.
>
> cheers
> Bruce
>
>
>
> On Fri, 7 Jun 2013, Joshua Lee wrote:
>
>  I'm trying to understand Leemput's subfield algorithm better as
>> implemented
>> in Freesurfer. Does the algorithm make use of intensity differences in the
>> internal hippocampal lamina from the subject's T1 image to warp meshes and
>> assign subfield probabilities? Or does it depend only on outward
>> boundaries
>> of the hippocampus and probability priors to determine the inner
>> boundaries
>> between CAs and dentate gyrus?
>> -
>> Josh
>>
>>
>>
>
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> 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
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Re: [Freesurfer] subfield algorithm and subject intensity differences

[Joshua Lee]

That is interesting and good to know. Thanks.

I am looking for a reference that provides validation metrics on the Van
Leemput (2010) method as implemented in Freesurfer. To your knowledge, is
there such a reference?

Best,

Joshua



On Fri, Jun 7, 2013 at 12:49 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

> Koen, please correct me if I'm wrong, but I'd say the answer is no.
> Since these tissue classes share the same Gaussian parameters, their
> likelihood term is the same, and the posterior is fully determined by
> the prior (i.e., the atlas).
> /E
>
>
>
> On Fri, 2013-06-07 at 12:42 -0700, Joshua Lee wrote:
> > Thanks Bruce and Eugenio,
> >
> >  Suppose I had two identical images of a subject, but in one image I
> > reduced the contrast of internal lamina while leaving the rest of the
> > image intact...just removing internal intensity differences, but
> > leaving the outer boundary contrast intact.
> >
> > Would the images result in very different subfield segmentations?
> >
> > Josh
> >
> >
> > -
> >
> > Joshua Lee
> >
> > Graduate Student
> > Center for Mind and Brain &
> >
> > Department of Psychology
> >
> > University of California, Davis
> > 530.747.3805
> >
> >
> > On Fri, Jun 7, 2013 at 12:33 PM, Bruce Fischl
> >  wrote:
> >     Hi Josh
> >
> > it depends on intensity differences if it can find them as
> > well as boundary/geometry.
> >
> > cheers
> > Bruce
> >
> >
> >
> > On Fri, 7 Jun 2013, Joshua Lee wrote:
> >
> > I'm trying to understand Leemput's subfield algorithm
> > better as implemented
> > in Freesurfer. Does the algorithm make use of
> > intensity differences in the
> > internal hippocampal lamina from the subject's T1
> > image to warp meshes and
> > assign subfield probabilities? Or does it depend only
> > on outward boundaries
> > of the hippocampus and probability priors to determine
> > the inner boundaries
> > between CAs and dentate gyrus?
> > -
> > Josh
> >
> >
> >
> >
> >
> > 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.
> >
> >
>
> --
> Juan Eugenio Iglesias, PhD
> http://www.jeiglesias.com
> igles...@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
>
>
>
>
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[Freesurfer] surface stream steps

[Joshua Lee]

Dear Freesurfers,

>From the Wiki Freesurfer surface stream follows something like:

   1. Affine registration to Tal.
   2. Bias correction and skull stripping
   3. Classify WM
   4. Cut hemisphere planes
   5. Tile WM surface
   6. Refine WM surface following GM-WM intensity gradients
   7. Nudge (nudge?) WM surface to follow the GM-CSF gradient to generate
   pial surface
   8. Labeling Data Set
   9. Stats

May I ask which couple of these steps tend to be the most computationally
taxing/longest to complete?

Also, I'm not sure I understand #7. Is the WM surface scaled in some sense
to approximate the GM-CSF boundary, or is this just a refinement step like
#6 of a surface that already approximates the GM-CSF boundary?

Thanks, I've spent most of my time working with the sub-cortical stream.
-
Joshua
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[Freesurfer] methods Q

[Joshua Lee]

Hi Experts,

I just wanted confirm my understanding that Freesurfer does not employ
multi-atlas label fusion methods. Is this correct?

Thanks,

Best,



Joshua




-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
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Re: [Freesurfer] methods Q

[Joshua Lee]

Thank you Bruce. That makes a lot of sense.

Josh


On Fri, Jun 14, 2013 at 5:59 AM, Bruce Fischl wrote:

> Hi Joshua
>
> we have such techniques (developed by Mert Sabuncu), but don't use them by
> default because(a) they are very slow, and (b) they would require us to
> distribute the manually labeled data which we don't have IRB approval for
> Bruce
>
>
>
> On Thu, 13 Jun 2013, Joshua Lee wrote:
>
>  Hi Experts,
>>
>> I just wanted confirm my understanding that Freesurfer does not employ
>> multi-atlas label fusion methods. Is this correct?
>>
>> Thanks,
>>
>> Best,
>>
>>
>>
>> Joshua
>>
>>
>>
>>
>> -
>> Joshua Lee
>> Graduate Student
>> Center for Mind and Brain &
>> Department of Psychology
>> University of California, Davis
>> 530.747.3805
>>
>>
>>
>
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> 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
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Re: [Freesurfer] How to avoid overlaps between volume labels?

[Joshua Lee]

Well you could  mri_binarize the three volumes, then subtract regions
using fslmaths from the FSL suite. Of course this would create gaps
between your formerly adjacent regions.


Joshua


-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis



On Tue, Jun 5, 2012 at 11:46 PM, Yuko Yotsumoto  wrote:
> Hello,
>
> With FreeSurfer v4.5, I have three functionally localized surface labels 
> (A.label, B.label, C.label), and converted this label to volume by using 
> mri_label2vol with --proj. I now have three volume labels, A.mgz, B.mgz, and 
> C.mgz.
>
> Because these three labels are adjacent to each other, [A.mgz and B.mgz] and 
> [B.mgz and C.mgz] share many voxels, and [A.mgz and C.mgz] also share a small 
> number of voxels, while there is no overlap in the surface labels.
>
> I'd like to make these volume labels independent by somehow creating boundary 
> into the volume so that each volume labels never share any voxels. What would 
> be the best way to do so? Is there anything I can do using a command line?
>
> Best,
> Yuko Yotsumoto
>
>
>
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[Freesurfer] Restart from somewhere in the middle of mri_ca_register

[Joshua Lee]

Is it possible/pracitcal? This is a long step, and unfortunately my
analysis computer was rebooted in the middle of this step, and I was hoping
to present the volumes tomorrow.. ouch.
-
Josh
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Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

[Joshua Lee]

not that I have any real hope  lol
-
Josh


On Mon, Jul 16, 2012 at 1:41 PM, Joshua Lee  wrote:

> Is it possible/pracitcal? This is a long step, and unfortunately my
> analysis computer was rebooted in the middle of this step, and I was hoping
> to present the volumes tomorrow.. ouch.
> -
> Josh
>
>
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Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

[Joshua Lee]

Yeah I didn't think so..well my fault for trying to push 30 brains through
at a time on just 24 cores and 24 Gigs of RAM, and all started within 10
minutes of each other..froze her up and locked others out. Ahh, well.
Thanks Bruce and crew!
-
Josh


On Mon, Jul 16, 2012 at 1:58 PM, Bruce Fischl wrote:

> no, sorry :<
>
> On Mon, 16 Jul 2012, Joshua Lee wrote:
>
>  Is it possible/pracitcal? This is a long step, and unfortunately my
>> analysis
>> computer was rebooted in the middle of this step, and I was hoping to
>> present the volumes tomorrow.. ouch.
>> -
>> Josh
>>
>>
>>
>>
>
> 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
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> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] subcortical gray matter volumes

[Joshua Lee]

In my data-set I have observed that Freesurfer has a tendency to include
some amygdala into the hippocampal head, despite a visible strip of alveus
white-matter segregating hippocampus from amygdala in my images. Has this
tendency been noticed by others? If so, has anyone found a non-manual
correction?
Best,
-
Josh

On Thu, Aug 2, 2012 at 7:37 AM, Bruce Fischl wrote:

> Hi Fred
>
> 1. Yes, this has been done multiple times, including in our original 2002
> paper:
> https://surfer.nmr.mgh.**harvard.edu/ftp/articles/**fischl02-labeling.pdf
>
> 2. You can manually edit, but it's a lot more work. In the cortex minor
> interventions can lead to large improvements in accuracy. Unfortunately we
> have no such algorithm subcortically. That said, things are usually quite
> accurate except in a small percentage of cases.
>
> cheers
> Bruce
>
>
>
> On Wed, 1 Aug 2012, Fred Sanders wrote:
>
>  Hi All,
>> Two questions:
>>
>> 1. I am interested in subcortical gray matter volumes such as hippocampus,
>> amygdala, & basal ganglia. Can someone recommend some good references
>> looking at the accuracy of Freesurfer relative to the "gold standard"
>> approach of hand-tracing these structures?
>>
>> 2. Most of the problems that require quality checks for Freesurfer relate
>> to
>> defining the cortical surface and the grey-white boundary.  As far as I
>> can
>> tell, there is rarely a need to edit Freesurfer's definitions of
>> subcortical
>> gray.  Am I correct in this?
>>
>>
>>
>> Thanks!
>> Fred
>>
>>
>>
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[Freesurfer] mri_convert downsample then resample shifts image upward one voxel

[Joshua Lee]

I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and then
again back up to 1mm isotropic space. The resultant image shifted up a
voxel from the original converted straght to nii.gz. This points to the
resampling procedure, and not the conversion to different file format.
Suggestions?

Note: I wanted to hand trace the hippocampus in the norm.mgz, and upsampled
the norm.mgz to trace on. I traced it, and then downsampled to 1mm to
compare with Freesurfer segmentation, but found it shifted.
Josh
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Re: [Freesurfer] mri_convert downsample then resample shifts image upward one voxel

[Joshua Lee]

I've isolated the problem to a fsl utility fslreorient2std I used to get
the brains to view right-side-up  in fslview. I don't get the error when
not using this utility. mri_convert is cleared, I think.
Josh

On Fri, Aug 10, 2012 at 8:15 AM, Douglas N Greve
wrote:

> what are your exact mri_convert commands?
> doug
>
> On 08/09/2012 06:05 PM, Joshua Lee wrote:
> > I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and
> > then again back up to 1mm isotropic space. The resultant image shifted
> > up a voxel from the original converted straght to nii.gz. This points
> > to the resampling procedure, and not the conversion to different file
> > format. Suggestions?
> >
> > Note: I wanted to hand trace the hippocampus in the norm.mgz, and
> > upsampled the norm.mgz to trace on. I traced it, and then downsampled
> > to 1mm to compare with Freesurfer segmentation, but found it shifted.
> > Josh
> >
> >
> >
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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[Freesurfer] mri_convert unsupported slice timing error

[Joshua Lee]

Hi All,

I tried to convert a high res T2 image using mri_convert and got this error
message:

nifti1Read(): unsupported slice timing pattern 5


Any advice? Complete message below:


mri_convert DKA2921c_20120807_001_003_t2_
tse_hippo.img bb.nii.gz

$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from 003_t2_tse_hippo.img...
nifti1Read(): unsupported slice timing pattern 5 in ./003_t2_tse_hippo.hdr

Joshua
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Re: [Freesurfer] mri_convert unsupported slice timing error

[Joshua Lee]

I started over from the .dcm and I didn't encounter the error anymore. So
alls well.
-
Josh


On Sun, Aug 19, 2012 at 11:54 PM, Joshua Lee  wrote:

> Hi All,
>
> I tried to convert a high res T2 image using mri_convert and got this
> error message:
>
> nifti1Read(): unsupported slice timing pattern 5
>
>
> Any advice? Complete message below:
>
>
> mri_convert DKA2921c_20120807_001_003_t2_
> tse_hippo.img bb.nii.gz
>
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading from 003_t2_tse_hippo.img...
> nifti1Read(): unsupported slice timing pattern 5 in ./003_t2_tse_hippo.hdr
>
> Joshua
>
>
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Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

[Joshua Lee]

Hi Everyone,

Back in May I was very excited to learn that there was some movement toward
allowing Freesurfer to utilize the higher than 1mm iso. resolutions of some
of our structural images, which could be fantastic help in subcortical
segmentations. Is this something that is still in the works for the next
release?

gratefully,

Joshua




-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Thu, May 31, 2012 at 5:49 PM, Bruce Fischl wrote:

> Hi Joshua
>
> sorry, I haven't found the time to really work on it. I spent a couple of
> hours and found some problems, but haven't found the time to fix them
>
> Bruce
>
> On Thu, 31 May 2012, Joshua Lee wrote:
>
>  Hi Bruce,
>>
>> I'm just checking in to see how it turned out with the subcortical
>> segmentation using the high resolution images I sent.
>> Best,
>>
>> Joshua
>>
>>
>>
>>
>>
>>
>> -
>> Joshua Lee
>> Graduate Student
>> Center for Mind and Brain &
>> Department of Psychology
>> University of California, Davis
>> 530.747.3805
>>
>>
>> On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl > >
>> wrote:
>>  you need to call mris_make_surfaces directly. It's a bit
>>  complicated as you need to intensity normalize and register the
>>  hires volume to the surfaces first. I have an example script if
>>  anyone is interested, but no one has used it yet but me I don't
>>  think (unless Matt Glasser has gotten his version working, which
>>  on second thought he probably has)
>>
>>  On Mon, 14 May 2012, Michael Waskom wrote:
>>
>>Hi Bruce,
>>Is there a flag for this on recon-all? áOr do you
>>
>>need to use
>>mri_make_surfaces directly?
>>
>>Best,
>>Michael
>>
>>On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl
>>
>>wrote:
>>á á áHi Joshua
>>
>>á á áyes, we already have upgraded
>>mris_make_surfaces to take higher
>>á á áres data
>>á á áand refine the surfaces with it. Haven't tried
>>it on the aseg
>>á á áyet, but if
>>á á áyou upload a sample dataset I could see how
>>hard it is.
>>
>>á á ácheers
>>á á áBruce
>>á á áOn Mon, 14 May 2012,
>>á á áJoshua Lee wrote:
>>
>>á á á> Dear Freesurfers,
>>á á á>
>>á á á> Over the last years, MR imaging technology
>>hasimproved such
>>á á áthat sub 1-mm
>>á á á> isotropic scans can be obtained with good
>>signal to noise
>>á á ácharacteristics.
>>á á á> For example, our lab uses 0.7mm isotropic
>>structural MR
>>á á áimages. I understand
>>á á á> that the Freesurfer pipeline will up-sample
>>these to 1mm
>>á á áisotropic, but it
>>á á á> seems a shame that so much information is
>>left unused which
>>á á ácould be used to
>>á á á> improve the accuracy of sub-cortical and
>>cortical
>>á á ásegmentation. My question
>>á á á> is whether there are any plans at Freesurfer
>>to change the
>>á á áreference
>>á á á> standard resolution from 1mm isotropic, or
>>provide another
>>á á ásolution that can
>>á á á> help researchers make the most of your
>>technology.
>>á á á>
>>á á á> Sincerely,
>>á á á>
>>á á á>
>>á á á> Joshua
>>á á á> -
>>á á á> Joshua
>>á á á>
>>á á á>
>>á á á>
>>
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>>
>>
>>The information in this e-mail is intended only for
>> 

[Freesurfer] Perirhinal Cortex ....how?

[Joshua Lee]

Can I get thickness values for the perirhinal (posterior parahipp too
maybe???)
I came across
http://surfer.nmr.mgh.harvard.edu/fswiki/PerirhinalArea35Labels but the
labels download link isn't existent. I tried running the commands on that
page anyway but of course it can't find the label...

Thanks for any info you may share

-
Josh
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Re: [Freesurfer] Perirhinal Cortex ....how?

[Joshua Lee]

In that case, I'll just wait the several weeks. That's great news BTW!
Thanks again for all your work.
Joshua
-



On Tue, Dec 11, 2012 at 6:12 PM, Bruce Fischl wrote:

> Hi Josh
> Perirhinal will be part of the upcoming 5.2 release in a few weeks. If you
> can't wait, nick can probably get you a beta
> Bruce
>
>
>
> On Dec 11, 2012, at 8:25 PM, Joshua Lee  wrote:
>
> Can I get thickness values for the perirhinal (posterior parahipp too
> maybe???)
> I came across
> http://surfer.nmr.mgh.harvard.edu/fswiki/PerirhinalArea35Labels but the
> labels download link isn't existent. I tried running the commands on that
> page anyway but of course it can't find the label...
>
> Thanks for any info you may share
>
> -
> Josh
>
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[Freesurfer] ooops deleted fsaverage

[Joshua Lee]

do I need to download the whole  freesurfer package again to get it?
-
Josh
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Re: [Freesurfer] Freesurfer 5.2 release date?

[Joshua Lee]

Thanks for all your hard work on the coming release. Is there a feature
list of whats in the new release? This would be helpful in deciding to wait
on a new project I'm about to start.
Thanks!
-
Josh


On Thu, Jan 3, 2013 at 5:37 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Note: Nick's response does not apply to tracula code, where changes can be
> expected until the night before the official release.
>
> On Thu, 3 Jan 2013, Nick Schmansky wrote:
>
> > Hi,
> >
> > A beta of the upcoming v5.2 is available here:
> >
> > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
> >
> > the hold-up has been getting the 64b mac lion build working, which has
> > been a challenge, but we're close.  I dont anticipate these posted linux
> > builds to change, so barring bugs that the public might find, we expect
> > the official release within two weeks.
> >
> > Nick
> >
> >
> >> Hi Folks,
> >> I just wanted to inquire about the estimated release date for Freesurfer
> >> 5.2 ?
> >> Is there a beta version we could try out ?
> >> Thanks
> >> Mehul
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> ___
> Freesurfer mailing list
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> 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
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Re: [Freesurfer] FW: longitudinal analysis

[Joshua Lee]

I dont know if this applies but I sometimes have really long run times when
image quality is bad, usually from subject movement. I drop them.
Josh

On Fri, Jan 18, 2013 at 1:31 PM, paul horton wrote:

> Hi Bruce and Martin,
>
> Thanks for your replies.
>
> With regards to the questions from Bruce,
>
> 1.The machine has 72gb of ram
> 2.There are no other processes running
> 3.There are 178 time points.
>
> With regards to the questions from Martin,
>
> 1. This is happening in the -long runs, but, only in 1 of the four runs of
> that subject.
> 2.  I have added a part of the log below.  I am not sure if its
> 'mris_volmask' or 'mri_aparc2aseg' running.
> #
>
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/mri
>
> mris_volmask --label_left_white 2 --label_left_ribbon 3
> --label_right_white 41 --label_right_ribbon 42 --save_ribbon
> --save_distance PREDEP46C_fsf.long.PREDEP46_template
>
> SUBJECTS_DIR is /home/k0933235/paul/PREDEP_Structural/subjects2
>
> loading input data...
>
> hemi masks overlap voxels = 533537
>
> writing volume
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/mri/ribbon.mgz
>
> writing ribbon files
>
> #-
>
> #@# AParc-to-ASeg Tue Jan 15 05:45:35 GMT 2013
>
>
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template
>
> mri_aparc2aseg --s PREDEP46C_fsf.long.PREDEP46_template --volmask
>
> reading colortable from annotation file...
>
> colortable with 36 entries read (originally
> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>
> reading colortable from annotation file...
>
> colortable with 36 entries read (originally
> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>
> SUBJECTS_DIR /home/k0933235/paul/PREDEP_Structural/subjects2
>
> subject PREDEP46C_fsf.long.PREDEP46_template
>
> outvol
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/mri/aparc+aseg.mgz
>
> useribbon 0
>
> baseoffset 0
>
> RipUnknown 0
>
> Reading lh white surface
>
>
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/surf/lh.white
>
> Reading lh pial surface
>
>
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/surf/lh.pial
>
> Loading lh annotations from
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/label/lh.aparc.annot
>
> Reading rh white surface
>
>
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/surf/rh.white
>
> Reading rh pial surface
>
>
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/surf/rh.pial
>
> Loading rh annotations from
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/label/rh.aparc.annot
>
> Have color table for lh white annotation
>
> Have color table for rh white annotation
>
> Loading ribbon segmentation from
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from
> /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/mri/aseg.mgz
>
> ASeg Vox2RAS: ---
>
> -1.000 0.000 0.000 128.000;
>
> 0.000 0.000 1.000 -128.000;
>
> 0.000 -1.000 0.000 128.000;
>
> 0.000 0.000 0.000 1.000;
>
> -
>
> Labeling Slice
>
> 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
>
> 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
>
> 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
> 
>
> Thanks
>
> Paul
> --
> Date: Fri, 18 Jan 2013 14:59:06 -0500
> From: mreu...@nmr.mgh.harvard.edu
> To: horton_p...@hotmail.com
> CC: al.hang...@yahoo.ca; Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FW: longitudinal analysis
>
>
> Hi Paul,
>
> also, is this happening in the -base run or in one of the -long runs (or
> in all of the -long runs of that subject). What binary is running so slowly
> (you mentioned some output "labelling slice", can you scroll up in the log
> and see what exactly is running)?
>
> Best, Martin
>
> On 01/18/2013 02:46 PM, Bruce Fischl wrote:
>
> how much RAM do you have in the machine? And are there other processes
> running at the same time? How many timepoints does the subject have?
>
> Bruce
>
> On Fri, 18 Jan 2013, paul horton wrote:
>
> Hi Alex,
>
> Thanks for your reply.
>
> I am also using Linux. I have restarted the analysis a few times but the
> process for this particular subject is very slow. When I try the same
> analysis on a different subject using the same machine, it only takes a
> few
> hours.  So not sure why the analysis is havi

Re: [Freesurfer] beta

[Joshua Lee]

Does this mean that using Freesurfer at sub-1mm isotropic resolutions will
not be possible next version?
Josh


On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky
wrote:

> Colin,
>
> It will still error if any dimension is greater than 256, which then means
> the flag -cw256 must be added to recon-all.  This flag chops dimensions
> greater than 256 down to 256.  The reason it doesnt do it automatically is
> that with this chopping, its not certain that it isnt removing into the
> head, so the user needs to be aware of this, so that they can inspect
> orig.mgz with freeview to make sure the head is fully visible.
>
> Nick
>
> > Does the beta permit volumes bigger than 256^3 voxels? just askingand
> > just asking about raw dimensions in unit-voxels at the start of pipeline
> >
> > cheers
> >
> > Colin
> >
> > On 18 January 2013 17:00, 
> 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-requ...@nmr.mgh.harvard.edu
> >>
> >> You can reach the person managing the list at
> >> freesurfer-ow...@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. v5.2.0 beta, round two (Nick Schmansky)
> >>2. Re: pial not computing (Borzello, Mia)
> >>3. Re: pial not computing (Bruce Fischl)
> >>4. Re: FW:  longitudinal analysis (Alex Hanganu)
> >>
> >>
> >> -- Forwarded message --
> >> From: Nick Schmansky 
> >> To: 
> >> Cc:
> >> Date: Fri, 18 Jan 2013 11:20:43 -0500
> >> Subject: [Freesurfer] v5.2.0 beta, round two
> >> For those willing and brave enough, another beta of v5.2.0 has been
> >> posted
> >> here for you to download and test:
> >>
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
> >>
> >> The Mac builds should work (note: the lion build is 64b, snow-leopard is
> >> 32b).
> >>
> >> The final release still awaits some critical improvements to the Tracula
> >> stream, but the main recon-all stream with this beta is final.  The
> >> final
> >> release is expected the first week of February.
> >>
> >> Freesurfer team
> >>
> >>
> >>
> >>
> >>
> >> -- Forwarded message --
> >> From: "Borzello, Mia" 
> >> To: "freesurfer@nmr.mgh.harvard.edu" 
> >> Cc:
> >> Date: Fri, 18 Jan 2013 16:25:40 +
> >> Subject: Re: [Freesurfer] pial not computing
> >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure
> >> how/where to run this and I don't see a page on the freesurfer site.
> >>
> >> Thanks so much,
> >> m
> >> 
> >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> >> Sent: Thursday, January 17, 2013 1:30 PM
> >> To: Borzello, Mia
> >> Cc: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] pial not computing
> >>
> >> Hi Mia
> >>
> >> this is fixed in the newest version. You can grab a new mris_topo_fixer
> >> and you rerun and it should be all set. You probably should take a look
> >> at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
> >> or skull attached, and the hemispherees successfully separated)
> >>
> >> cheers
> >> Bruce
> >> On Thu, 17
> >> Jan 2013, Borzello, Mia wrote:
> >>
> >> > Okay, so it didn't complete without error. I've attached the
> >> recon-all.log. Also, I was using another post op patient's MRI scans.
> >> >
> >> > thanks so much,
> >> > m
> >> > 
> >> > From: freesurfer-boun...@nmr.mgh.harvard.edu [
> >> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
> >> fis...@nmr.mgh.harvard.edu]
> >> > Sent: Thursday, January 17, 2013 11:22 AM
> >> > To: Borzello, Mia
> >> > Cc: freesurfer@nmr.mgh.harvard.edu
> >> > Subject: Re: [Freesurfer] pial not computing
> >> >
> >> > Hi Mia
> >> >
> >> > we need to see the recon-all.log. Did it end with an error?
> >> > Bruce
> >> > On Thu, 17 Jan
> >> > 2013, Borzello, Mia wrote:
> >> >
> >> >> Hi Freesurfers,
> >> >>
> >> >> I just ran a recon, and it seems that only  the lh.pial computed, but
> >> not the rh.pial. What would be the cause of this?
> >> >> Thanks,
> >> >> m
> >> >>
> >> >> ___
> >> >> 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
> >>
> >>
> >>
> >>
> >> -- Forwarded message --
> >> From: Bruce Fischl 
> >> To: "Borzello, Mia" 
> >> Cc: "freesurfer@nmr.mgh.harvard

Re: [Freesurfer] beta

[Joshua Lee]

Thanks Bruce. That sounds great. Will subcortical segmentations also
benefit yet. I remember that you once told me that there were some problems
with it.
-
Josh


On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl
wrote:

> Hi Josh
>
> the way we are handling sub-mm data is to run it through the standard
> recon-all, then run a postprocessing surface deformation on the higher res
> data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs.
>
> cheers
> Bruce
>
>
>
> On Mon, 21 Jan 2013, Joshua Lee wrote:
>
>  Does this mean that using Freesurfer at sub-1mm isotropic resolutions
>> will not be possible next version?
>> Josh
>>
>>
>> On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky <
>> ni...@nmr.mgh.harvard.edu> wrote:
>>   Colin,
>>
>>   It will still error if any dimension is greater than 256, which
>> then means
>>   the flag -cw256 must be added to recon-all.  This flag chops
>> dimensions
>>   greater than 256 down to 256.  The reason it doesnt do it
>> automatically is
>>   that with this chopping, its not certain that it isnt removing into
>> the
>>   head, so the user needs to be aware of this, so that they can
>> inspect
>>   orig.mgz with freeview to make sure the head is fully visible.
>>
>>   Nick
>>
>>   > Does the beta permit volumes bigger than 256^3 voxels? just
>> askingand
>>   > just asking about raw dimensions in unit-voxels at the start of
>> pipeline
>>   >
>>   > cheers
>>   >
>>   > Colin
>>   >
>>   > On 18 January 2013 17:00, > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>   >> or, via email, send a message with subject or body 'help' to
>>   >> 
>> freesurfer-requ...@nmr.mgh.**harvard.edu
>>   >>
>>   >> You can reach the person managing the list at
>>   >> 
>> freesurfer-ow...@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. v5.2.0 beta, round two (Nick Schmansky)
>>   >>2. Re: pial not computing (Borzello, Mia)
>>   >>3. Re: pial not computing (Bruce Fischl)
>>   >>4. Re: FW:  longitudinal analysis (Alex Hanganu)
>>   >>
>>   >>
>>   >> -- Forwarded message --
>>   >> From: Nick Schmansky 
>>   >> To: 
>> 
>> >
>>   >> Cc:
>>   >> Date: Fri, 18 Jan 2013 11:20:43 -0500
>>   >> Subject: [Freesurfer] v5.2.0 beta, round two
>>   >> For those willing and brave enough, another beta of v5.2.0 has
>> been
>>   >> posted
>>   >> here for you to download and test:
>>   >>
>>   >> ftp://surfer.nmr.mgh.harvard.**edu/pub/dist/freesurfer/5.2.0-**
>> BETA/ <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/>
>>   >>
>>   >> The Mac builds should work (note: the lion build is 64b,
>> snow-leopard is
>>   >> 32b).
>>   >>
>>   >> The final release still awaits some critical improvements to the
>> Tracula
>>   >> stream, but the main recon-all stream with this beta is final.
>>  The
>>   >> final
>>   >> release is expected the first week of February.
>>   >>
>>   >> Freesurfer team
>>   >>
>>   >>
>>   >>
>>   >>
>>   >>
>>   >> -- Forwarded message --
>>   >> From: "Borzello, Mia" 
>>   >> To: 
>> "freesur...@nmr.mgh.harvard.**edu"
>> >
>>   >> Cc:
>>   >> Date: Fri, 18 Jan 2013 16:25:40 +
>>   &g

Re: [Freesurfer] beta

[Joshua Lee]

This news is most unfortunate. We all appreciate the Freesurfer team's
work. Freesurfer, and project's like these, provide a substantial
multiplier effect to the productivity of the neuroscience community. There
should be more funding for these types of neuroscience research
infrastructure.
-
Joshua


On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl wrote:

> Hi Ed
>
> I mean that the grant funding FreeSurfer maintainance didn't get renewed.
> We certainly will continue support and development, but it does have a
> substantial negative impact on the engineering we can do, such as getting
> rid of the 1mm restrictions.
>
> cheers
> Bruce
>
>
>
> On Wed, 30 Jan 2013, Ed Gronenschild wrote:
>
>  Hi Bruce,
>> What do you mean: no support anymore or no new development?
>>
>> Cheers,
>> Ed
>>
>> On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:
>>
>>   Message: 7
>>   Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
>>   From: Bruce Fischl 
>>   Subject: Re: [Freesurfer] beta
>>   To: Colin Reveley 
>>   Cc: Joshua Lee
>>   , 
>> freesurf**e...@nmr.mgh.harvard.edu
>> ,
>>  Nick Schmansky 
>>   Message-ID:
>>  > mgh.harvard.edu
>> >
>>   Content-Type: text/plain; charset="iso-8859-1"
>>
>>   Hi Colin
>>
>>   yes, but we simply don't have the person power to do it at the
>>   moment. Our
>>   FS support grant ends in a month and is not going to get
>>   renewed, so it's
>>   going to be hard to do anytime soon.
>>
>>   sorry
>>   Bruce
>>
>>
>>
>>
> ___
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>
>
> 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.
>
>
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[Freesurfer] upsampling aseg.mgz to dimension and spacing

[Joshua Lee]

I would like to upsample the aseg.mgz to

Dimensions: 370X512X512
Spacing 0.5mm in x,y, and z.

Any suggestions?
-
Josh
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Re: [Freesurfer] upsampling aseg.mgz to dimension and spacing

[Joshua Lee]

forgot to mention, this is to upsample Freesurfer Aseg to compare with
manually traced hipp volumes from original structural images.
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Mon, Feb 4, 2013 at 11:15 AM, Joshua Lee  wrote:

> I would like to upsample the aseg.mgz to
>
> Dimensions: 370X512X512
> Spacing 0.5mm in x,y, and z.
>
> Any suggestions?
> -
> Josh
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] upsampling aseg.mgz to dimension and spacing

[Joshua Lee]

I do indeed. Thank you very much!
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Mon, Feb 4, 2013 at 11:19 AM, Bruce Fischl wrote:

> Hi Josh
>
> do you have a volume with those dimensions? If so, you can use
>
> -rl  -rt nearest
>
> cheers
> Bruce
>
>
> On Mon, 4 Feb 2013, Joshua Lee wrote:
>
>  I would like to upsample the aseg.mgz to
>>
>> Dimensions: 370X512X512
>> Spacing 0.5mm in x,y, and z.
>>
>> Any suggestions?
>> -
>> Josh
>>
>>
>>
>
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[Freesurfer] when aseg fails

[Joshua Lee]

Hi All,

I'm just wondering what kind of protocol people are using to address
the situation when Freesurfer has a catastrophic failure in accurately
segmenting the sub-cortical structures.  While manual editing is an
option, are there upstream changes that might improve the subcortical
segmentation is re-run (e.g. wm control points?). Drop them? If
conducting an analysis of Freesurfer subcortical segmentation in some
population, how have people handled these cases?

Thanks,

Josh
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[Freesurfer] dual installation question

[Joshua Lee]

If I want to install the new Freesurfer version but retain the older
Freesurfer install as well, what issues might I face?
Is it simply sourcing the usual setup scripts?

export FREESURFER_HOME=/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

-
Josh
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Re: [Freesurfer] dual installation question

[Joshua Lee]

Thanks.
Best,
-
Josh


On Thu, Feb 21, 2013 at 10:05 AM, Shantanu Ghosh <
shant...@nmr.mgh.harvard.edu> wrote:

> Or you may have multiple freesurfer versions within the freesurfer
> director, something like
> /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc.
> and then
> export FREESURFER_HOME=/freesurfer/5.1
> etc
> Hth, S.
>
>
> On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote:
> > Hi Josh,
> > you can modify the SetUpFreeSurfer.sh to source the correct version.
> > Hth, Shantanu
> >
> > On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote:
> >> If I want to install the new Freesurfer version but retain the older
> >> Freesurfer install as well, what issues might I face?
> >> Is it simply sourcing the usual setup scripts?
> >>
> >> export FREESURFER_HOME=/freesurfer
> >> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> >>
> >> -
> >> Josh
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > --
> > Shantanu Ghosh, Ph.D.
> > Harvard Medical School & Massachusetts General Hospital
> > Martinos Center for Biomedical Imaging
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
>
>
> --
> Shantanu Ghosh, Ph.D.
> Harvard Medical School & Massachusetts General Hospital
> Martinos Center for Biomedical Imaging
>
>
>
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Re: [Freesurfer] Hippocampus volume calculations

[Joshua Lee]

I have noticed that Freesurfer tends to include white matter in superior
hippocampus (e.g. alveus), perhaps this is not included in the
hipposubfields volumes?

Wondering, if I were to take a hand traced hippocampus rename it to
aseg.mgz, and made sure that the label matched what Freesurfer expects,
would the hipposubfields algorithm do its magic on this volume?
Joshua


Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga <
gariko...@gmail.com> wrote:

> Thanks Juan Eugenio,
> we have visually inspected the segmentations, and we observe that the
> volume differences between aseg and hippo-subfields are constants among
> subjects, and consistent in both left and right hemispheres (please see
> table attached, columns diff.aseg.left.subfields and 
> diff.aseg.right.subfields).
> Indeed, the percentage of the difference between the aseg and the
> hippo-subfields is about 20% average (19.5% for the left and 22.1% for the
> right hemisphere), and there are not strong differences at the individual
> subject level.
>
> The aseg values always are bigger than the hippo-subfields across all
> planes (please see attached photos with some examples). And, as it can be
> seen in the attached pictures, the hippo-subfield segmentation seems to be
> more accurate than the aseg one.
>
> We used the standard recon-all procedure with -hippo-subfields -qcache -all
>
> Considering that these differences are pretty consistent across subjects,
> Do you think that there is anything wrong with our results? Or anything
> that we are missing in our analysis?
>
> Thank you very much,
> Gari
>
>
> [image: Inline image 1]
>
>
>
>
>
>
>
>
>
>
>
> On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias <
> igles...@nmr.mgh.harvard.edu> wrote:
>
>> Dear Gari,
>> The subfield module uses a different, independent method to segment the
>> hippocampus, and consistency with ASEG results is not explicitly
>> enforced. That said, the subfield module is inialialized with the ASEG,
>> and the results should be pretty close to each other, for the most part.
>> Have you visually inspected the segmentation for those cases in which
>> the difference looks large?
>> Thanks,
>> /Eugenio
>>
>>
>> On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote:
>> > Hi,
>> > I am calculating hippocampus volumes with 5.2 in CentOS 4.
>> >
>> >
>> > I compare volumes (the same apply for lh and for rh) when calculating
>> > as:
>> > > Left.Hippocampus value in 1mm3 from aseg.stats
>> > > I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
>> > obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in
>> > order to get mm3, and sum every column except
>> > left_hippocampal_fissure.
>> >
>> >
>> > I obtain quite different values, for example:
>> >
>> >  row.names
>> >   lh.aseg
>> >lhHIP
>> >   rh.aseg
>> >rhHIP
>> > 1
>> > S_00
>> > 4848.8
>> > 3828.187
>> > 4878.8
>> > 3767.739
>> > 2
>> > S_02
>> > 4153.8
>> > 3371.517
>> > 4547.6
>> > 3389.918
>> >
>> >
>> > Am I doing anything wrong? Should I calculate the hippos subfields
>> > volumes differently?
>> >
>> >
>> >
>> > Many thanks!
>> > Gari
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>>
>> -
>> Juan Eugenio Iglesias, PhD
>> http://www.jeiglesias.com
>> igles...@nmr.mgh.harvard.edu
>> Athinoula A. Martinos Center for Biomedical Imaging
>> Department of Radiology, MGH, Harvard Medical School
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, Massachusetts 2129
>> U.S.A.
>>
>>
>>
>>
>> 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 info

[Freesurfer] 3T MPRage flags

[Joshua Lee]

The new Freesurfer has an optional flag to adjust NU intensity correction
parameters for images acquired on 3T scanners. There exists also a  flag
for MPRage sequences.

I use 3T MPRages. What is the recommended use in this case?

Thanks
Josh
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[Freesurfer] subcortical atlases

[Joshua Lee]

Hello Freesurfer Gurus,

I was wondering whether the original individual subject atlases used to
construct the probabilistic atlases for subcortical segmentation have been
made available for download?
Thanks!
josh
-
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Re: [Freesurfer] subcortical atlases

[Joshua Lee]

I understand. Thank you Bruce, for you good work.
Joshua

-
Joshua Lee
Doctoral Candidate
Department of Psychology &
Center for Mind and Brain
University of California, Davis
530.747.3805


On Wed, Jun 4, 2014 at 5:53 PM, Bruce Fischl 
wrote:

> Hi Josh
>
> sorry, it was impossible to get IRB approval for such a thing given that
> the data was collected a long time ago by various people.
>
> sorry
> Bruce
>
>
> On Wed, 4 Jun 2014, Joshua Lee wrote:
>
> > Hello Freesurfer Gurus,
> >
> > I was wondering whether the original individual subject atlases used to
> construct the probabilistic atlases for
> > subcortical segmentation have been made available for download?
> > Thanks!
> > josh
> > -
> >
> >
> >
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[Freesurfer] protocol question

[Joshua Lee]

Dear Freesurfer Experts,

I am trying to better understand what regions of the hippocampal formation
are meant to be included in the hippocampal label (e.g. inclusion of the
alveus/fornix, lateral boundaries around the subiculum, superior boundaries
in the tail, etc.).

Has the protocol used to manually segment the hippocampus for the
Freesurfer atlases been described in detail somewhere? I cannot seem to
locate a specific reference.

Thanks

Joshua
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[Freesurfer] Hippocampal Sub-Field Segmentation -Appropriate Scan Protocol to Use

[Joshua Lee]

Dear Experts,

I've been collecting hi-res hippocampal scans with a 32 ch coil on a 3T
Siemens Trio to manually segment hippocampal subfields. However, I wonder
whether the protocol is appropriate for use with the new Freesurfer subfield
segmentation tool.

Specifically, our hi-res scan does not capture the entire brain, rather it
acquires slices perpendicular to the long axis just for the length of the
long axis axis. Can this scan be used for the new subfield
auto-segmentation? Or does it require a whole-brain acquisition?

We do acquire a 1 mm isotropic whole brain MPRage, but...

Thanks for any info,
Joshua
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[Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

[Joshua Lee]

Are there any existing Amazon EC2 AMI registered publicly that can be used?
I want to analyze a lot of data fast.

Thanks,
-
Joshua Lee
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Re: [Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

[Joshua Lee]

I think I may have found it as a public ami with freesurfer 5.1. Testing it
out on Bert right now. Thanks!!
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


2011/10/30 Joshua Lee 

> I think I may have found it as a public ami with freesurfer 5.1. Testing
> it out on Bert right now. Thanks!!
> -
> Joshua Lee
>
>
>
> 2011/10/28 Joshua Lee 
>
>> Thanks Pedro, that's fantastic!  I'm still getting used to the ec2 thing.
>> Is there a password Ill need for root access?
>> Thanks,
>>
>> Josh
>> -
>> Joshua Lee
>> Graduate Student
>> Center for Mind and Brain &
>> Department of Psychology
>> University of California, Davis
>> 530.747.3805
>>
>>
>>
>> 2011/10/28 Pedro Paulo de Magalhães Oliveira Junior > >
>>
>>> I have one. I'll give you the link
>>>
>>> -- iOS 5.0
>>>
>>> Em 28/10/2011, às 20:52, Joshua Lee  escreveu:
>>>
>>> Are there any existing Amazon EC2 AMI registered publicly that can be
>>> used? I want to analyze a lot of data fast.
>>>
>>> Thanks,
>>> -
>>> Joshua Lee
>>>
>>> ___
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>>>
>>>
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>>> properly
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>>>
>>>
>>
>
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[Freesurfer] Error During Talairach Transform

[Joshua Lee]

#@# Talairach Failure Detection Wed Nov  2 02:03:32 EDT 2011
/home/virtualuser/freesurfer/subjects/test005/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

I am receiving the error (pasted below) on about half of my scans, despite
all cans using same protocol. I detect no obvious issue with the quality of
the images. I have original dicoms, and am using mri_convert to save into a
single .mgz (or .nii, doesn't neem to make a difference), and the
unpredictability of the error makes diagnosis problematic. TKMedit2 reveals
absolutely wacky registrations. I am processing on Freesurfer 5.1, and have
replicated issue on two different installations. I am designing a new
longitudinal study inheriting the same imaging protocol and I do not want
to get in a situation demanding manual editing of the talairach. Can anyone
help me out? Thanks, Joshua

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0030, pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux

recon-all -s test005 exited with ERRORS at Wed Nov  2 02:03:32 EDT 2011

For more details, see the log file
/home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
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Re: [Freesurfer] Error During Talairach Transform

[Joshua Lee]

Small Update: Error Disappears if Using Freesurfer version 5.0 instead of
5.1. However, since I am keenly interested in the hippocampal-subfield
segmentation capabilities of the most recent version, I am loathe to
regress to an earlier version of FreeSurfer
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee  wrote:

> #@# Talairach Failure Detection Wed Nov  2 02:03:32 EDT 2011
> /home/virtualuser/freesurfer/subjects/test005/mri
>
>  talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>
> I am receiving the error (pasted below) on about half of my scans, despite
> all cans using same protocol. I detect no obvious issue with the quality of
> the images. I have original dicoms, and am using mri_convert to save into a
> single .mgz (or .nii, doesn't neem to make a difference), and the
> unpredictability of the error makes diagnosis problematic. TKMedit2 reveals
> absolutely wacky registrations. I am processing on Freesurfer 5.1, and have
> replicated issue on two different installations. I am designing a new
> longitudinal study inheriting the same imaging protocol and I do not want
> to get in a situation demanding manual editing of the talairach. Can anyone
> help me out? Thanks, Joshua
>
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0030, pval=0. < threshold=0.0050)
> Manual Talairach alignment may be necessary, or
> include the -notal-check flag to skip this test,
> making sure the -notal-check flag follows -all
> or -autorecon1 in the command string.
> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
> 2009 i686 GNU/Linux
>
> recon-all -s test005 exited with ERRORS at Wed Nov  2 02:03:32 EDT 2011
>
> For more details, see the log file
> /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> -
> Joshua Lee
> Graduate Student
> Center for Mind and Brain &
> Department of Psychology
> University of California, Davis
> 530.747.3805
>
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Re: [Freesurfer] Hippocampal Sub-Field Segmentation

[Joshua Lee]

Thats an interesting suggestion, givien my recently reported issues with
the talairach in FreeSurfer 5.1.
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Wed, Nov 2, 2011 at 11:41 AM, Bruce Fischl wrote:

> I believe so, but Koen is the one who would know for sure
>
> Bruce
>
> On Wed, 2 Nov 2011, Alan Francis wrote:
>
>  Hello Bruce et al,
>>
>> I have a dataset processed in 5.0. Can I use the Hippocampal Sub-Field
>> Segmentation tools of 5.1 to process these?
>>
>> thanks so much,
>>
>> Alan
>>
>> BIDMC/ Psychiatry
>>
>>
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Re: [Freesurfer] Error During Talairach Transform

[Joshua Lee]

Thanks Nick,

Is use-mritotal equivalent to what version 5.0 does by default?

Also,  any suggestions on why this talairach error would occur only on a
portion of my data, despite all being collected with the same imaging
protocol, same conversions from dicom, etc?
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky wrote:

> joshua,
>
> try adding -use-mritotal to the end of your recon-all command.  it will
> use an alternate way to compute the talairach.xfm which works better on
> some data.
>
> the change from v5.0 to v5.1 in the talairach stage was that in v5.1,
> the talairach.xfm is needed to compute nu.mgz, so the talairach stage
> needs to precede the nu_correct stage.  this means the talairach stage
> can no longer use nu.mgz as input, which seems to work better than
> orig.mgz for some data (and is the case for your data).
>
> in the next release of freesurfer, recon-all will automatically try the
> alternate method (mritotal) if the default talairach_avi method fails
> the tal-check.
>
> n.
>
>
> On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote:
> > can you send us an example that works in 5.0 and fails in 5.1?
> >
> > thanks
> > Bruce
> > On Wed, 2 Nov
> > 2011, Joshua Lee wrote:
> >
> > > Small Update: Error Disappears if Using Freesurfer version 5.0 instead
> of
> > > 5.1. However, since I am keenly interested in the hippocampal-subfield
> > > segmentation capabilities of the most recent version, I am loathe to
> regress
> > > to an earlier version of FreeSurfer
> > > -
> > > Joshua Lee
> > > Graduate Student
> > > Center for Mind and Brain &
> > > Department of Psychology
> > > University of California, Davis
> > > 530.747.3805
> > >
> > >
> > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee  wrote:
> > >   #@# Talairach Failure Detection Wed Nov  2 02:03:32 EDT 2011
> > >   /home/virtualuser/freesurfer/subjects/test005/mri
> > >
> > >talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> > >
> > >   I am receiving the error (pasted below) on about half of my
> > >   scans, despite all cans using same protocol. I detect no obvious
> > >   issue with the quality of the images. I have original dicoms,
> > >   and am using mri_convert to save into a single .mgz (or .nii,
> > >   doesn't neem to make a difference), and the unpredictability of
> > >   the error makes diagnosis problematic. TKMedit2 reveals
> > >   absolutely wacky registrations. I am processing on Freesurfer
> > >   5.1, and have replicated issue on two different installations. I
> > >   am designing a new longitudinal study inheriting the same
> > >   imaging protocol and I do not want to get in a situation
> > >   demanding manual editing of the talairach. Can anyone help me
> > >   out? Thanks, Joshua
> > >
> > >   ERROR: talairach_afd: Talairach Transform:
> > >   transforms/talairach.xfm ***FAILED*** (p=0.0030, pval=0. <
> > >   threshold=0.0050)
> > >   Manual Talairach alignment may be necessary, or
> > >   include the -notal-check flag to skip this test,
> > >   making sure the -notal-check flag follows -all
> > >   or -autorecon1 in the command string.
> > >   See
> > >   http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> > >   Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
> > >   01:57:59 UTC 2009 i686 GNU/Linux
> > >
> > >   recon-all -s test005 exited with ERRORS at Wed Nov  2 02:03:32
> > >   EDT 2011
> > >
> > >   For more details, see the log file
> > >
> /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log
> > >   To report a problem, see
> > >   http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > >
> > >   -
> > > Joshua Lee
> > > Graduate Student
> > > Center for Mind and Brain &
> > > Department of Psychology
> > > University of California, Davis
> > > 530.747.3805
> > >
> > >
> > >
> > >
> > ___ Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> The information in this e-mail 

Re: [Freesurfer] Error During Talairach Transform

[Joshua Lee]

OK, now I understand better.
One further question: Would the use of MRI-total degrade quality of the
Freesurfer segmentations substantively, and would using it only on a
portion of my data introduce a systematic bias to the data set?
Josh



On Wed, Nov 2, 2011 at 4:15 PM, Nick Schmansky wrote:

> no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1
> uses orig.mgz.
>
> its hard to say why it would fail for some subjects but not others,
> other than head positioning and to some degree ventricle size makes a
> difference.
>
> n.
>
> On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
> > Thanks Nick,
> >
> > Is use-mritotal equivalent to what version 5.0 does by default?
> >
> > Also,  any suggestions on why this talairach error would occur only on
> > a portion of my data, despite all being collected with the same
> > imaging protocol, same conversions from dicom, etc?
> > -
> >
> > Joshua Lee
> >
> > Graduate Student
> > Center for Mind and Brain &
> >
> > Department of Psychology
> >
> > University of California, Davis
> > 530.747.3805
> >
> >
> > On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky
> >  wrote:
> > joshua,
> >
> > try adding -use-mritotal to the end of your recon-all
> > command.  it will
> > use an alternate way to compute the talairach.xfm which works
> > better on
> > some data.
> >
> > the change from v5.0 to v5.1 in the talairach stage was that
> > in v5.1,
> > the talairach.xfm is needed to compute nu.mgz, so the
> > talairach stage
> > needs to precede the nu_correct stage.  this means the
> > talairach stage
> > can no longer use nu.mgz as input, which seems to work better
> > than
> > orig.mgz for some data (and is the case for your data).
> >
> > in the next release of freesurfer, recon-all will
> > automatically try the
> > alternate method (mritotal) if the default talairach_avi
> > method fails
> > the tal-check.
> >
> > n.
> >
> >
> >
> > On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote:
> > > can you send us an example that works in 5.0 and fails in
> > 5.1?
> > >
> > > thanks
> > > Bruce
> > > On Wed, 2 Nov
> > > 2011, Joshua Lee wrote:
> >         >
> > > > Small Update: Error Disappears if Using Freesurfer version
> > 5.0 instead of
> > > > 5.1. However, since I am keenly interested in the
> > hippocampal-subfield
> > > > segmentation capabilities of the most recent version, I am
> > loathe to regress
> > > > to an earlier version of FreeSurfer
> > > > -
> > > > Joshua Lee
> > > > Graduate Student
> > > > Center for Mind and Brain &
> > > > Department of Psychology
> > > > University of California, Davis
> > > > 530.747.3805
> > > >
> > > >
> > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee
> >  wrote:
> > > >   #@# Talairach Failure Detection Wed Nov  2 02:03:32
> > EDT 2011
> > > >   /home/virtualuser/freesurfer/subjects/test005/mri
> > > >
> > > >talairach_afd -T 0.005 -xfm
> > transforms/talairach.xfm
> > > >
> > > >   I am receiving the error (pasted below) on about
> > half of my
> > > >   scans, despite all cans using same protocol. I
> > detect no obvious
> > > >   issue with the quality of the images. I have
> > original dicoms,
> > > >   and am using mri_convert to save into a single .mgz
> > (or .nii,
> > > >   doesn't neem to make a difference), and the
> > unpredictability of
> > > >   the error makes diagnosis problematic. TKMedit2
> > reveals
> > > >   absolutely wacky registrations. I am processing on
> > Freesurfer
> > > >   5.1, and have replicated issue on two different
> > installations. I
> >

Re: [Freesurfer] Error During Talairach Transform

[Joshua Lee]

Dear FreeSurfur Gurus,
It appears that the using -use-mritotal worked to get past the talairach
error.

 Thank you for all your help. We really appreciate it.

Joshua




On Wed, Nov 2, 2011 at 7:01 PM, Bruce Fischl wrote:

> Hi Michael
>
> we found that the conversion to unsigned character sometimes compressed
> the brain into only a couple of bits of the dynamic range. We know use the
> talairach xform to locate the center of the brain and make sure that a ball
> centered at the tal origin occupies a lot of the histogram. This helped in
> a number of cases, but maybe the makes the tal xform more sensitive to bias
> fields and strange intensity scalings.
>
> Bruce
>
> On Wed, 2 Nov 2011, Michael Waskom wrote:
>
>  Hi,
>> What was the reason for this switch?  Intuitively it seems that a
>> bias-corrected image is likely to get a better registration (since I
>> assume the target has essentially uniform intensities).
>>
>> Michael
>>
>> On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky 
>> wrote:
>>  no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas
>> v5.1
>>  uses orig.mgz.
>>
>>  its hard to say why it would fail for some subjects but not others,
>>  other than head positioning and to some degree ventricle size makes a
>>  difference.
>>
>>  n.
>>
>> On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
>> > Thanks Nick,
>> >
>> > Is use-mritotal equivalent to what version 5.0 does by default?
>> >
>> > Also,  any suggestions on why this talairach error would occur only on
>> > a portion of my data, despite all being collected with the same
>> > imaging protocol, same conversions from dicom, etc?
>> > -
>> >
>> > Joshua Lee
>> >
>> > Graduate Student
>> > Center for Mind and Brain &
>> >
>> > Department of Psychology
>> >
>> > University of California, Davis
>> > 530.747.3805
>> >
>> >
>> > On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky
>> >  wrote:
>> > joshua,
>> >
>> > try adding -use-mritotal to the end of your recon-all
>> > command.  it will
>> > use an alternate way to compute the talairach.xfm which works
>> > better on
>> > some data.
>> >
>> > the change from v5.0 to v5.1 in the talairach stage was that
>> > in v5.1,
>> > the talairach.xfm is needed to compute nu.mgz, so the
>> > talairach stage
>> > needs to precede the nu_correct stage.  this means the
>> > talairach stage
>> > can no longer use nu.mgz as input, which seems to work better
>> > than
>> > orig.mgz for some data (and is the case for your data).
>> >
>> >     in the next release of freesurfer, recon-all will
>> > automatically try the
>> > alternate method (mritotal) if the default talairach_avi
>> > method fails
>> > the tal-check.
>> >
>> > n.
>> >
>> >
>> >
>> > On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote:
>> >     > can you send us an example that works in 5.0 and fails in
>> > 5.1?
>> > >
>> > > thanks
>> > > Bruce
>> > > On Wed, 2 Nov
>> > > 2011, Joshua Lee wrote:
>> >         >
>> > > > Small Update: Error Disappears if Using Freesurfer version
>> > 5.0 instead of
>> > > > 5.1. However, since I am keenly interested in the
>> > hippocampal-subfield
>> > > > segmentation capabilities of the most recent version, I am
>> > loathe to regress
>> > > > to an earlier version of FreeSurfer
>> > > > -
>> > > > Joshua Lee
>> > > > Graduate Student
>> > > > Center for Mind and Brain &
>> > > > Department of Psychology
>> > > > University of California, Davis
>> > > > 530.747.3805
>> > > >
>> > > >
>> > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee
>> >  wrote:
>> > > >   #@# Talairach Failure Detection Wed Nov  2 02:03:32
>> > EDT 2

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Joshua Lee]

Thanks again Pedro. I just ran 220 brains through in day or two using the
cloud. Fantastic.
The script people have been talking about would have been useful.
One thing I didn't realize was that I should have moved the freesurfer
subject directory from /usr/local/freesurfer/subjects to the larger disk
that comes with the instance. I had disk-write errors because the the main
partition ran out of space.

Anyway, ec2 rocks with Freesurfer.
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


2011/11/12 Nolan Nichols 

> If only running a small number of instances, I think it is reasonable
> to leave the ami w/o a .license file since it is easy enough to scp it
> up to the cloud. For running a cluster it would be nice to have a
> script, perhaps using Fabric, to upload a .license file to each
> instance in a cluster. As it stands, the starcluster FS AMI does not
> have a .license file and requires one to be uploaded manually.
>
> Nolan
>
> 2011/11/12 Thomas Ballinger :
> > Perhaps the AMI image could be without a licence file and uploading one
> > (acquired though normal means) would be required?  (I suppose that's the
> > basic solution we're looking for a clean way around)
> >
> > 2011/11/12 Pedro Paulo de Magalhães Oliveira Junior <
> p...@netfilter.com.br>
> >>
> >> Maybe we can set up a web server in the Martinos center and the AMI
> Image
> >> can authenticate in it.
> >> -
> >> Pedro Paulo de Magalhães Oliveira Junior
> >> Netfilter & SpeedComm Telecom
> >> -- www.netfilter.com.br
> >> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> >>
> >>
> >>
> >>
> >> On Sat, Nov 12, 2011 at 15:28, Nick Schmansky <
> ni...@nmr.mgh.harvard.edu>
> >> wrote:
> >>>
> >>> I'm happy to see the work getting the cloud to be feasible. I still
> need
> >>> to catch up on this thread but one issue that I'd like to sort out is
> >>> tracking the license count.  Its fine for a new user to use an existing
> >>> image, but I think there will need to be a way to remind people to
> request
> >>> our .license file even if they don't actually use the file so that
> cloud
> >>> usages get counted (license count is critical for us for grant renewal
> >>> purposes). Ideas on a clean way to do this?
> >>> N.
> >>>
> >>> On Nov 12, 2011, at 11:10 AM, Thomas Ballinger
> >>>  wrote:
> >>>
> >>> Satra, the ipython example looks great. The scripts I posted also use
> >>> fabric for running Freesurfer, but don't download Freesurfer due to it
> >>> already being installed on Pedro's image. I agree with Satra that
> >>> individually administered instances might work better for those
> wishing to
> >>> run a few cases with Freesurfer, particularly due to the predictable
> long
> >>> running time (lessening the benefits of job distribution) and ability
> of a
> >>> recon-all job to efficiently use all of a ec2 small instance's cpu. I
> think
> >>> starcluster is pretty awesome, and I would love to push people in that
> >>> direction, but it won't be quite as push-button, and the benefits may
> be
> >>> minimal for small use cases.  That's not to say there aren't plenty of
> folks
> >>> who would rather use Nolan's solution (me for one :))
> >>> Tom
> >>>
> >>>
> >>> On Sat, Nov 12, 2011 at 9:14 AM, Nolan Nichols  wrote:
> >>>>
> >>>> Hi Satra,
> >>>>
> >>>> Fabric does look nice, thanks for pointing it out and for a link to
> the
> >>>> ipython_in_a_box example.
> >>>>
> >>>> That framework might work for what I had in mind for freesurfer and
> >>>> starcluster, which uses the same idea to keep the initial AMI
> footprint
> >>>> smaller/flexible.
> >>>>
> >>>> Cheers,
> >>>>
> >>>> Nolan
> >>>>
> >>>> On Nov 12, 2011 7:32 AM, "Satrajit Ghosh"  wrote:
> >>>>>
> >>>>> hi nolan,
> >>>>> i think starcluster is a great way to create a cluster on aws. but
> for
> >>>>> those wanting to create a single instance and install things on a

Re: [Freesurfer] Freesurfer on Windows!

[Joshua Lee]

I'd try reinstalling virtualbox. Then I'd make sure that you adjust the vm
with enough ram, videocard memory, etc. It should work fine. I run the same
setup all the time, and I don't believe that this is a 'known issue'.

Joshua



On Mon, Nov 14, 2011 at 8:25 AM, wrote:

> Hello Friends,
>
> I am a newcomer to freesurfer and wanted to use it in windows. I
> downloaded as instructed the
>
> freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi-for windows
>
> the virtual box version is 4.1.6
>
> and installed with the required settings as mentioned in your website. I
> tried it in two systems one with
> a windows xp, 4 GB RAM, Intel Core Quad CPU, 2,40 GhZ, 64 bit system
> and the other system Windows 7, Intel Xeon 2.53 Ghz(2 processors), 24 Gb
> RAM, 64 bit system
>
> In both the sytems i was able to configure the virtual box for the xubuntu
> linux but it starts and progress bar in the middle and then the
> application closes without any errors. Is this a known problem? Am i
> missing something?
>
> Thanking you
>
> With regards
> Dr.-Ing M.Muthuraman
> Klinik für Neurology
> Schittenhelmstrasse 10
> Kiel-24105
> Germany.
>
> ___
> Freesurfer mailing list
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> 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.
>
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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.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Joshua Lee]

It would be great if Freesurfer maintained an official AMI. One important
reason to do so is security. If the AMI is maintained by the organization,
then people can feel reassured that their data is not being downloaded to a
compromised instance, not that any on this board would have such malicious
intent. Moreover, it could contain such scripts as makes the analysis
process easier.

-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


2011/11/14 Pedro Paulo de Magalhães Oliveira Junior 

> Ok. I'll label as private this AMI that has .license file.
>
> Maybe we can make a tutorial on how to create an AMI instead.
>
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
>
> On Mon, Nov 14, 2011 at 21:07, Nick Schmansky 
> wrote:
>
>> Glad to hear it works well.  To revisit the issue of the license (in the
>> form of the .license file which needs to be in the $FREESURFER_HOME
>> directory and the request of which is used for usage tracking), I think
>> the convention to follow for any publicly available AMI freesurfer
>> instances should be to not include a .license file with it, so as to
>> force the download of this file (so that freesurfer usage will be
>> tracked).  A user need only do this once for however many times they use
>> the cloud instance.
>>
>> N.
>>
>> On Mon, 2011-11-14 at 17:16 -0500, Joshua Lee wrote:
>> > Thanks again Pedro. I just ran 220 brains through in day or two using
>> > the cloud. Fantastic.
>> > The script people have been talking about would have been useful.
>> > One thing I didn't realize was that I should have moved the freesurfer
>> > subject directory from /usr/local/freesurfer/subjects to the larger
>> > disk that comes with the instance. I had disk-write errors because the
>> > the main partition ran out of space.
>> >
>> > Anyway, ec2 rocks with Freesurfer.
>> > -
>> >
>> > Joshua Lee
>> >
>> > Graduate Student
>> > Center for Mind and Brain &
>> >
>> > Department of Psychology
>> >
>> > University of California, Davis
>> > 530.747.3805
>> >
>> >
>> > 2011/11/12 Nolan Nichols 
>> > If only running a small number of instances, I think it is
>> > reasonable
>> > to leave the ami w/o a .license file since it is easy enough
>> > to scp it
>> > up to the cloud. For running a cluster it would be nice to
>> > have a
>> > script, perhaps using Fabric, to upload a .license file to
>> > each
>> > instance in a cluster. As it stands, the starcluster FS AMI
>> > does not
>> > have a .license file and requires one to be uploaded manually.
>> >
>> > Nolan
>> >
>> > 2011/11/12 Thomas Ballinger :
>> >
>> > > Perhaps the AMI image could be without a licence file and
>> > uploading one
>> > > (acquired though normal means) would be required?  (I
>> > suppose that's the
>> > > basic solution we're looking for a clean way around)
>> > >
>> > > 2011/11/12 Pedro Paulo de Magalhães Oliveira Junior
>> > 
>> > >>
>> > >> Maybe we can set up a web server in the Martinos center and
>> > the AMI Image
>> > >> can authenticate in it.
>> > >>
>> >
>> -
>> > >> Pedro Paulo de Magalhães Oliveira Junior
>> > >> Netfilter & SpeedComm Telecom
>> > >> -- www.netfilter.com.br
>> > >> -- For
>> > mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> On Sat, Nov 12, 2011 at 15:28, Nick Schmansky
>> > 
>> > >> wrote:
>> > >>>
>> > >>> I'm happy to see the work getting the cloud to be
>> > feasible. I still need
>> 

Re: [Freesurfer] Hippocampal Sub field segmentation

[Joshua Lee]

At least by my reading of the Duvernoy Human Hippocampus atlas, the most
anterior and posterior extents of the hippocmapus (perhaps just a slice at
the tips in most scans) are almost entirely composed of the CA1 subfield.
Thoughts?

Joshua
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis



On Thu, Nov 17, 2011 at 6:46 AM, Alan Francis wrote:

> Thanks Koen.
>
>
> On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput <
> k...@nmr.mgh.harvard.edu> wrote:
>
>> The answer is close to what Shashwath suggested, except that the
>> "Hippocampus" segmentation is really computed at the same time as all
>> the other subfields. For unfortunate reasons, the tail of the
>> hippocampus that is not further subdivided in our manual training
>> segmentations was called "Hippocampus" for lack of other good names -
>> it really should have been "Part of the Hippocampus Tail that We
>> Didn't Subdivide Manually".
>>
>> If you want to compute the total volume of the hippocampus, you'll
>> need to add the volume of this part, though..
>>
>> Hope this helps,
>>
>> Koen
>>
>>
>> On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis 
>> wrote:
>> > Thanks Shashwath.
>> >
>> > On Wed, Nov 16, 2011 at 2:04 PM, Shashwath 
>> wrote:
>> >>
>> >> Alan- I believe the label "hippocampus" here refers to the remaining
>> hippo
>> >> segment after the algorithm has completed  labelling of all subfields.
>> In
>> >> essence this would not be a measure that conveys very meaningful info.
>> >>
>> >> Sent from my iPhone
>> >>
>> >> On Nov 16, 2011, at 1:01 PM, Alan Francis 
>> >> wrote:
>> >>
>> >> > Hi Koen and FreeSurfers:
>> >> >
>> >> > I have a 3T dataset that has undergone processing using 5.1. I have
>> also
>> >> > run the Hippo sub fields command. Here are my results:
>> >> >
>> >> > [root@NeuroImage-Gamma mri]# kvlQuantifyPosteriorProbabilityImages
>> >> > $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt
>> posterior_right_*
>> >> > posterior_Right-Hippocampus.mgz
>> >> >
>> >> > volumeInVoxels:
>> >> > right_CA1: 2473.34
>> >> > right_CA2-3: 7530.08
>> >> > right_CA4-DG: 4160.99
>> >> > right_fimbria: 520.14
>> >> > right_hippocampal_fissure: 376.772
>> >> > right_presubiculum: 2780.65
>> >> > right_subiculum: 4230.04
>> >> > Right-Hippocampus: 2277.69
>> >> >
>> >> > My question is :  Since these are "subfields" of the Hippocampus,
>> should
>> >> > not the sum of all subregions  be equal the volume of the Right
>> Hippocampus?
>> >> >
>> >> > Thanks so much!
>> >> >
>> >> > Alan Francis
>> >> >
>> >> > Beth Israel Deaconess Medical Center, BOSTON
>> >> >
>> >> > ___
>> >> > Freesurfer mailing list
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>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >
>> >> >
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Re: [Freesurfer] Hippocampal Sub field segmentation

[Joshua Lee]

There is great variability between the different segmentation protocols
used by different research groups, and I think people are eager for a
standard to facilitate comparison and replication. By becoming part of
Freesurfer, I suspect that your segmentation algorithm will become that
standard.

Luckily, I think it is one of truest I've seen to conforming to the
Duvernoy atlas. Whether Duvernoy's work is the appropriate standard I am
not qualified to say, but he does seem to be cited quite often as the basis
for the various protocols in the wild. However, there might still be some
differences between Duvernoy and the scheme used by the Freesurfer subfield
segmentation.

Particularly, Duvernoy seems to indicate that in the head and the tail CA1
seems to be the only subfield present in the anterior 1/3 of the head and
posterior 1/3 of the tail. Looking coronally, subiculum seems to extend
further laterally in the head and tail than in the body of the hippocampus.
Lastly, CA1 seems to continue further medially on the superior side of the
hippocampus in the head and tail than in body. CA3, by my reading of
Duvernoy, seems to be tiny in the head and tail.

All these are fairly minor points. Still, I wouldn't mind some comments on
these observations, as they were changes I have been proposing to make in
the segmentation protocol used in my lab.

Best,


Joshua

Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Thu, Nov 17, 2011 at 9:30 AM, Koen Van Leemput
wrote:

> Hi Joshua,
>
> I'm not a neuroanatomist so I can't really answer that question. My
> aim has just been to replicate what a human expert has given us as
> segmentation examples on a number of different subjects.
>
> I know that different labs follow very different conventions for
> labeling the subfields manually. Perhaps someone else can chime in?
>
> Koen
>
>
> On Thu, Nov 17, 2011 at 12:18 PM, Joshua Lee  wrote:
> > At least by my reading of the Duvernoy Human Hippocampus atlas, the most
> > anterior and posterior extents of the hippocmapus (perhaps just a slice
> at
> > the tips in most scans) are almost entirely composed of the CA1 subfield.
> > Thoughts?
> >
> > Joshua
> > -
> > Joshua Lee
> > Graduate Student
> > Center for Mind and Brain &
> > Department of Psychology
> > University of California, Davis
> >
> >
> >
> > On Thu, Nov 17, 2011 at 6:46 AM, Alan Francis 
> > wrote:
> >>
> >> Thanks Koen.
> >>
> >> On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput
> >>  wrote:
> >>>
> >>> The answer is close to what Shashwath suggested, except that the
> >>> "Hippocampus" segmentation is really computed at the same time as all
> >>> the other subfields. For unfortunate reasons, the tail of the
> >>> hippocampus that is not further subdivided in our manual training
> >>> segmentations was called "Hippocampus" for lack of other good names -
> >>> it really should have been "Part of the Hippocampus Tail that We
> >>> Didn't Subdivide Manually".
> >>>
> >>> If you want to compute the total volume of the hippocampus, you'll
> >>> need to add the volume of this part, though..
> >>>
> >>> Hope this helps,
> >>>
> >>> Koen
> >>>
> >>>
> >>> On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis <
> alandarkene...@gmail.com>
> >>> wrote:
> >>> > Thanks Shashwath.
> >>> >
> >>> > On Wed, Nov 16, 2011 at 2:04 PM, Shashwath 
> >>> > wrote:
> >>> >>
> >>> >> Alan- I believe the label "hippocampus" here refers to the remaining
> >>> >> hippo
> >>> >> segment after the algorithm has completed  labelling of all
> subfields.
> >>> >> In
> >>> >> essence this would not be a measure that conveys very meaningful
> info.
> >>> >>
> >>> >> Sent from my iPhone
> >>> >>
> >>> >> On Nov 16, 2011, at 1:01 PM, Alan Francis  >
> >>> >> wrote:
> >>> >>
> >>> >> > Hi Koen and FreeSurfers:
> >>> >> >
> >>> >> > I have a 3T dataset that has undergone processing using 5.1. I
> have
> >>> >> > also
> >>> >> > run the Hippo sub fields command. Here are my results:
> >>> >> 

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Joshua Lee]

When I used the AMI, (maybe not Pedro's), so I sftp'd a license file to
each instance prior to running an analysis. Not a big deal. I didn't get a
new license for each instance, but copied the same one to multiple
instances.

Joshua

2011/11/18 Pedro Paulo de Magalhães Oliveira Junior 

> I have restored the image: 060244368407/FREESURFER51
>
> I'll create a web service that can log the number of instances spawned. Is
> that ok with you?
>  -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
>
> 2011/11/18 Bruce Fischl 
>
>> Hi PPJ,
>>
>> I would rather people use FS without licenses than find themselves unable
>> to use it, so why not leave it for now. Can you put a request that they
>> first download a license or register on your website? Alternatively, can
>> you just remove the .license file from the AMI forcing the users to get one?
>>
>> thanks for making this available
>> Bruce
>>
>>
>>
>> On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>>
>>  As requested I removed the AMI image because that image contains a
>>> .license file.
>>> I can republish the image when we find a solution for the licensing
>>> issue.
>>>
>>> --**--**
>>> -
>>> Pedro Paulo de Magalhães Oliveira Junior
>>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
>>>
>>> -- For mobile: http://itunes.apple.**com/br/artist/netfilter/**
>>> id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441>
>>>
>>>
>>>
>>>
>>> 2011/11/15 Joshua Lee 
>>>  It would be great if Freesurfer maintained an official AMI. One
>>> important reason to do so is security. If the
>>>  AMI is maintained by the organization, then people can feel
>>> reassured that their data is not being downloaded to
>>>  a compromised instance, not that any on this board would have such
>>> malicious intent. Moreover, it could contain
>>>  such scripts as makes the analysis process easier.
>>>
>>>  -
>>> Joshua Lee
>>> Graduate Student
>>> Center for Mind and Brain &
>>> Department of Psychology
>>> University of California, Davis
>>> 530.747.3805
>>>
>>>
>>> 2011/11/14 Pedro Paulo de Magalhães Oliveira Junior <
>>> p...@netfilter.com.br>
>>>  Ok. I'll label as private this AMI that has .license file.
>>> Maybe we can make a tutorial on how to create an AMI instead.
>>> --**--**
>>> -
>>> Pedro Paulo de Magalhães Oliveira Junior
>>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
>>>
>>> -- For mobile: http://itunes.apple.**com/br/artist/netfilter/**
>>> id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441>
>>>
>>>
>>>
>>>
>>> On Mon, Nov 14, 2011 at 21:07, Nick Schmansky 
>>> wrote:
>>>  Glad to hear it works well.  To revisit the issue of the license
>>> (in the
>>>  form of the .license file which needs to be in the $FREESURFER_HOME
>>>  directory and the request of which is used for usage tracking), I
>>> think
>>>  the convention to follow for any publicly available AMI freesurfer
>>>  instances should be to not include a .license file with it, so as to
>>>  force the download of this file (so that freesurfer usage will be
>>>  tracked).  A user need only do this once for however many times
>>> they use
>>>  the cloud instance.
>>>
>>>  N.
>>>
>>>
>>>
>>>
>>>
>>
>> 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<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.
>>
>
>
&

Re: [Freesurfer] Virtual Box crashes

[Joshua Lee]

Sounds like a virtualbox problem. Try reinstalling Virtualbox.. Try adding
a bit more video memory to the vm.
BTW, is there an error message, or does it just silently shut down?
-
Joshua


On Mon, Nov 21, 2011 at 2:05 AM, Popescu, V.  wrote:

>  Dear all, 
>
> Please help with the following problem: I am trying to run the FreeSurfer
> disk image on Virtual Box 4.1.6. I start it, I get: “GRUB loading please
> wait…” and then the Virtual Box crashes.
>
> It has 2048 MB base memory, 12 MB video memory. 
>
> Thank you!
>
> Veronica
>
> ** **
>
> ** **
>
> ___
> 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.
>
>
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Re: [Freesurfer] Virtual Box crashes

[Joshua Lee]

Sorry, your error message image is too small to read.
-
Josh

On Mon, Nov 21, 2011 at 9:04 AM, Popescu, V.  wrote:

>  Hi, Joshua!
>
> This is what I get on screen: 
>
> 
>
> I’ll try reinstalling the VB and see what happens. 
>
> Thank you!
>
> Best,
>
> Veronica
>
> ** **
>
> ** **
>  --
>
> *From:* nimzodisas...@gmail.com [mailto:nimzodisas...@gmail.com] *On
> Behalf Of *Joshua Lee
> *Sent:* maandag 21 november 2011 17:20
> *To:* Popescu, V.
> *Cc:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Virtual Box crashes
>
> ** **
>
> Sounds like a virtualbox problem. Try reinstalling Virtualbox.. Try adding
> a bit more video memory to the vm.
> BTW, is there an error message, or does it just silently shut down?
> 
>
> -
>
> Joshua
>
> ** **
>
> On Mon, Nov 21, 2011 at 2:05 AM, Popescu, V.  wrote:***
> *
>
> Dear all, 
>
> Please help with the following problem: I am trying to run the FreeSurfer
> disk image on Virtual Box 4.1.6. I start it, I get: “GRUB loading please
> wait…” and then the Virtual Box crashes.
>
> It has 2048 MB base memory, 12 MB video memory. 
>
> Thank you!
>
> Veronica
>
>  
>
>  
>
>
> ___
> 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
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> dispose of the e-mail.
>
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Re: [Freesurfer] Virtual Box crashes

[Joshua Lee]

Im a little lost. Are you running a 32 or 64 bit virtual machine? Is the
host 32 bit or 64 bit? The guest can never exceed the host, I believe. I
may be wrong.
Have you tried re-downloading the virtualbox image with Freesurfer?
Josh

On Tue, Nov 22, 2011 at 1:19 AM, Popescu, V.  wrote:

> **
>
> ** **
>
> Thank you very much for the help. It’s just the Window telling me that VB
> had to shut down and it’s very sorry on top of the VM dark screen with
> “GRUB loading please wait…”. I have attached the picture. 
>
> In the meantime I reinstalled the VBox but the same happens, and I get the
> following from the log file (last line): 
>
> 00:00:05.183 Read exceeds file size offStart=2397122560 cbToTransfer=1024
> cbFile=1056027568.
>
> It does complain that I allocated too much memory to the VM (exceeds 50%
> of the computer size). On the host there is room enough. I tried memory
> ballooning but it doesn’t work (no 64-bits host). 
>
> Thank you!
>
> Best,
>
> Veronica
>
> ** **
>
> ** **
>  --
>
> *From:* nimzodisas...@gmail.com [mailto:nimzodisas...@gmail.com] *On
> Behalf Of *Joshua Lee
> *Sent:* dinsdag 22 november 2011 3:45
>
> *To:* Popescu, V.
> *Cc:* **freesurfer@nmr.mgh.harvard.edu**
> *Subject:* Re: [Freesurfer] Virtual Box crashes
> 
>
>  ** **
>
> Sorry, your error message image is too small to read.
> 
>
> -
>
> Josh
>
> ** **
>
> On Mon, Nov 21, 2011 at 9:04 AM, Popescu, V.  wrote:***
> *
>
> Hi, Joshua!
>
> This is what I get on screen: 
>
> 
>
> I’ll try reinstalling the VB and see what happens. 
>
> Thank you!****
>
> Best,
>
> Veronica
>
>  
>
>  
>  --
>
> *From:* nimzodisas...@gmail.com [mailto:nimzodisas...@gmail.com] *On
> Behalf Of *Joshua Lee
> *Sent:* maandag 21 november 2011 17:20
> *To:* Popescu, V.
> *Cc:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Virtual Box crashes
>
>  
>
> Sounds like a virtualbox problem. Try reinstalling Virtualbox.. Try adding
> a bit more video memory to the vm.
> BTW, is there an error message, or does it just silently shut down?
> 
>
> -
>
> Joshua
>
>  
>
> On Mon, Nov 21, 2011 at 2:05 AM, Popescu, V.  wrote:***
> *
>
> Dear all, 
>
> Please help with the following problem: I am trying to run the FreeSurfer
> disk image on Virtual Box 4.1.6. I start it, I get: “GRUB loading please
> wait…” and then the Virtual Box crashes.
>
> It has 2048 MB base memory, 12 MB video memory. 
>
> Thank you!
>
> Veronica
>
>  
>
>  
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
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>  
>
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[Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

Hi All,

I would like to determine the volumes of a segmented region below or above
an arbitrary line in one of the planes. For example, what would be the
remaining volume of a label when z >= nth slice, where I would have
previously determined the appropriate value of n.



Thanks,
Josh
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Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

OK, I think I can take the output of binarize and then use FSL's fslroi
tool to split up on my plane, the find the volume of that final
mask...that will work as long as the output of binarize is in the same
space as its input.?.


On Wed, Nov 23, 2011 at 8:12 AM, Joshua Lee  wrote:

> Hi All,
>
> I would like to determine the volumes of a segmented region below or above
> an arbitrary line in one of the planes. For example, what would be the
> remaining volume of a label when z >= nth slice, where I would have
> previously determined the appropriate value of n.
>
>
>
> Thanks,
> Josh
>
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Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

Hey Doug, THanks. That looks simpler. I'll probably use that.

Question: Will the total volume of a ROI taken from aseg.mgz correspond to
the volume given in aseg.stats?

Josh



On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve
wrote:

> If you have matlab, you can load the aseg into matlab, like
> aseg = MRIread('aseg.mgz');
> vol = length(aseg.vol(:,:,n:256) == ID);
> where ID is the code number for the ROI you want  as found in
> $FREESURFER_HOME/**FreeSurferColorLUT.txt
> doug
>
> Joshua Lee wrote:
>
>> Hi All,
>>
>> I would like to determine the volumes of a segmented region below or
>> above an arbitrary line in one of the planes. For example, what would be
>> the remaining volume of a label when z >= nth slice, where I would have
>> previously determined the appropriate value of n.
>>
>>
>>
>> Thanks,
>> Josh
>> --**--**
>> 
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

Hi Bruce,

I'll see if I can phrase this right

In aseg.mgz each region has essentially been given a unique number (e.g. 17
for left hippocampus, for example). ROI taken from aseg.mgz volumes are
non-probabilistic, yes-no affairs already.  MRI_binarize just pulls this
out when we want to look at particular regions, say left hipp???

Josh





On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl wrote:

> probably not, as the aseg.stats calculation uses partial volume estimates.
>
> cheers
> Bruce
>
> On Wed, 30 Nov 2011, Joshua Lee wrote:
>
>  Hey Doug, THanks. That looks simpler. I'll probably use that.
>>
>> Question: Will the total volume of a ROI taken from aseg.mgz correspond to
>> the volume given in aseg.stats?
>>
>> Josh
>>
>>
>>
>> On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu>
>> wrote:
>>  If you have matlab, you can load the aseg into matlab, like
>>  aseg = MRIread('aseg.mgz');
>>  vol = length(aseg.vol(:,:,n:256) == ID);
>>  where ID is the code number for the ROI you want  as found in
>>  $FREESURFER_HOME/**FreeSurferColorLUT.txt
>>  doug
>>
>>  Joshua Lee wrote:
>> Hi All,
>>
>> I would like to determine the volumes of a segmented region
>> below or above an arbitrary line in one of the planes. For
>> example, what would be the remaining volume of a label when z >=
>> nth slice, where I would have previously determined the
>> appropriate value of n.
>>
>>
>>
>> Thanks,
>> Josh
>> --**--**
>> 
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop: 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>
>>
>>
>> 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<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.
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Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

I'm glad you caught that because I suddenly got really confused! Thank
Bruce for all your hard work!
Josh
-


On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl wrote:

> oops, I meant the aseg.stats, not the aseg.mgz
>
> On Wed, 30 Nov 2011, Joshua Lee wrote:
>
>  Hi Bruce,
>>
>> I'll see if I can phrase this right
>>
>> In aseg.mgz each region has essentially been given a unique number (e.g.
>> 17
>> for left hippocampus, for example). ROI taken from aseg.mgz volumes are
>> non-probabilistic, yes-no affairs already.  MRI_binarize just pulls this
>> out
>> when we want to look at particular regions, say left hipp???
>>
>> Josh
>>
>>
>>
>>
>> On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl > >
>> wrote:
>>  probably not, as the aseg.stats calculation uses partial volume
>>  estimates.
>>
>>  cheers
>>  Bruce
>>
>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>
>>  Hey Doug, THanks. That looks simpler. I'll probably use
>>  that.
>>
>>  Question: Will the total volume of a ROI taken from
>>  aseg.mgz correspond to
>>  the volume given in aseg.stats?
>>
>>  Josh
>>
>>
>>
>>  On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve
>>  
>>  wrote:
>>   If you have matlab, you can load the aseg into
>>  matlab, like
>>   aseg = MRIread('aseg.mgz');
>>   vol = length(aseg.vol(:,:,n:256) == ID);
>>   where ID is the code number for the ROI you want  as
>>  found in
>>   $FREESURFER_HOME/**FreeSurferColorLUT.txt
>>   doug
>>
>>   Joshua Lee wrote:
>>  Hi All,
>>
>>  I would like to determine the volumes of a segmented
>>  region
>>  below or above an arbitrary line in one of the planes. For
>>  example, what would be the remaining volume of a label
>>  when z >=
>>  nth slice, where I would have previously determined the
>>  appropriate value of n.
>>
>>
>>
>>  Thanks,
>>  Josh
>>  --**--**
>> 
>>
>>  __**_
>>  Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>>  --
>>  Douglas N. Greve, Ph.D.
>>  MGH-NMR Center
>>  gr...@nmr.mgh.harvard.edu
>>  Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>>  Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>  FileDrop:
>>  
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>
>>
>>
>>  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<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.
>>
>>
>>
>>
>>
>>
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Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

Actually, I have one last-last question.
If I use mri_binarize on my aseg.mgz file, does it remain in the same
'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz,
will that z -coordinate still be valid in nifti file i'd have mri-Binarize
create?

Josh


On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee  wrote:

> I'm glad you caught that because I suddenly got really confused! Thank
> Bruce for all your hard work!
> Josh
> -
>
>
> On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl 
> wrote:
>
>> oops, I meant the aseg.stats, not the aseg.mgz
>>
>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>
>>  Hi Bruce,
>>>
>>> I'll see if I can phrase this right
>>>
>>> In aseg.mgz each region has essentially been given a unique number (e.g.
>>> 17
>>> for left hippocampus, for example). ROI taken from aseg.mgz volumes are
>>> non-probabilistic, yes-no affairs already.  MRI_binarize just pulls this
>>> out
>>> when we want to look at particular regions, say left hipp???
>>>
>>> Josh
>>>
>>>
>>>
>>>
>>> On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>  probably not, as the aseg.stats calculation uses partial volume
>>>  estimates.
>>>
>>>  cheers
>>>  Bruce
>>>
>>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>>
>>>  Hey Doug, THanks. That looks simpler. I'll probably use
>>>  that.
>>>
>>>  Question: Will the total volume of a ROI taken from
>>>  aseg.mgz correspond to
>>>  the volume given in aseg.stats?
>>>
>>>  Josh
>>>
>>>
>>>
>>>  On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve
>>>  
>>>  wrote:
>>>   If you have matlab, you can load the aseg into
>>>  matlab, like
>>>   aseg = MRIread('aseg.mgz');
>>>   vol = length(aseg.vol(:,:,n:256) == ID);
>>>   where ID is the code number for the ROI you want  as
>>>  found in
>>>   $FREESURFER_HOME/**FreeSurferColorLUT.txt
>>>   doug
>>>
>>>   Joshua Lee wrote:
>>>  Hi All,
>>>
>>>  I would like to determine the volumes of a segmented
>>>  region
>>>  below or above an arbitrary line in one of the planes. For
>>>  example, what would be the remaining volume of a label
>>>  when z >=
>>>  nth slice, where I would have previously determined the
>>>  appropriate value of n.
>>>
>>>
>>>
>>>  Thanks,
>>>  Josh
>>>  --**--**
>>> 
>>>
>>>  __**_
>>>  Freesurfer mailing list
>>>  Freesurfer@nmr.mgh.harvard.edu
>>>  
>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>
>>>
>>>  --
>>>  Douglas N. Greve, Ph.D.
>>>  MGH-NMR Center
>>>  gr...@nmr.mgh.harvard.edu
>>>  Phone Number: 617-724-2358 Fax: 617-726-7422
>>>
>>>  Bugs: 
>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>>  FileDrop:
>>>  
>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>>
>>>
>>>
>>>  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<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.
>>>
>>>
>>>
>>>
>>>
>>>
>
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Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

Since it has be reiterated many times that aseg.stats is calulated using
estimates of partial volumes that increase accuracy over obtaining volumes
from binarized masks, I wonder whether I might still incorporate this
advanced procedure while still bisecting a previous segmentation by some
arbitrary plane, say z=27.

I propose the following procedure as an example for splitting the left
amygdala (for example) and still using the partial volume estimation:


   1. Make copies of aseg.mgz, one each for the partial segmentation you
   want to create (e.g. aseg_anterior.mgz and aseg_posterior.mgz, to split the
   amygdala by the plane z =27 on some particular brain, by some particular
   protocol).
   2. Edit  aseg_posterior.mgz (e.g. by tkmedit) to remove all amygdala
   anterior to z = 27. Similarly edit aseg_anterior.mgz to remove posterior
   segments.
   3. Run the stats on these edited segmentations, and record the data in
   aseg_posterior.stats and aseg_anterior.stats

Does this sound reasonable and wise procedure? If so, is there a quick way
to remove the unwanted segmentations without manually using a brush, slice
by slice in tkmedit? Loading it into Matlab, like Doug suggests, would
allow the edits I think, but then I'd have to rewrite the file from
matlab.. I think.

Josh





On Wed, Nov 30, 2011 at 2:49 PM, Bruce Fischl wrote:

> yes
>
> On Wed, 30 Nov 2011, Joshua Lee wrote:
>
>  Actually, I have one last-last question.
>> If I use mri_binarize on my aseg.mgz file, does it remain in the same
>> 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz,
>> will
>> that z -coordinate still be valid in nifti file i'd have mri-Binarize
>> create?
>>
>> Josh
>>
>>
>> On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee  wrote:
>>  I'm glad you caught that because I suddenly got really confused!
>>  Thank Bruce for all your hard work!
>>  Josh
>>  -
>>
>>
>> On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl
>>  wrote:
>>  oops, I meant the aseg.stats, not the aseg.mgz
>>
>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>
>>  Hi Bruce,
>>
>>  I'll see if I can phrase this right
>>
>>  In aseg.mgz each region has essentially been given a
>>  unique number (e.g. 17
>>  for left hippocampus, for example). ROI taken from
>>  aseg.mgz volumes are
>>  non-probabilistic, yes-no affairs already.
>>  MRI_binarize just pulls this out
>>  when we want to look at particular regions, say left
>>  hipp???
>>
>>  Josh
>>
>>
>>
>>
>>  On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl
>>  
>>  wrote:
>>   probably not, as the aseg.stats calculation
>>  uses partial volume
>>   estimates.
>>
>>   cheers
>>   Bruce
>>
>>  On Wed, 30 Nov 2011, Joshua Lee wrote:
>>
>>   Hey Doug, THanks. That looks simpler. I'll
>>  probably use
>>   that.
>>
>>   Question: Will the total volume of a ROI taken
>>  from
>>   aseg.mgz correspond to
>>   the volume given in aseg.stats?
>>
>>   Josh
>>
>>
>>
>>   On Wed, Nov 30, 2011 at 9:55 AM, Douglas N
>>      Greve
>>   
>>   wrote:
>>If you have matlab, you can load the aseg
>>  into
>>   matlab, like
>>aseg = MRIread('aseg.mgz');
>>vol = length(aseg.vol(:,:,n:256) == ID);
>>where ID is the code number for the ROI
>>  you want  as
>>   found in
>>$FREESURFER_HOME/**FreeSurferColorLUT.txt
>>doug
>>
>>Joshua Lee wrote:
>>   Hi All,
>>
>>   I would like to determine the volumes of a
>>  segmented
>>   region
>>   below or above an arbitrary line in one of the
>>  planes. For
>>   example, what would be the remaining volume of
>>  a label
>>   when z >=
>>   nth slice, where I would have previously
>>  determined the
>>   appropriate value of n.
>>
>>
>>
>>   Thanks,
>>   Josh
>>
>>   -**--**
>> -
>>
>>   _**__
>>   Freesurfer mailing list
>>   freesur..

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

[Joshua Lee]

Forgive me, I hadn't realize that tkmedit had a fill a function. I can do
what I propsed easily. Thanks again!
-
Joshua

On Thu, Dec 1, 2011 at 11:15 AM, Joshua Lee  wrote:

> Since it has be reiterated many times that aseg.stats is calulated using
> estimates of partial volumes that increase accuracy over obtaining volumes
> from binarized masks, I wonder whether I might still incorporate this
> advanced procedure while still bisecting a previous segmentation by some
> arbitrary plane, say z=27.
>
> I propose the following procedure as an example for splitting the left
> amygdala (for example) and still using the partial volume estimation:
>
>
>1. Make copies of aseg.mgz, one each for the partial segmentation you
>want to create (e.g. aseg_anterior.mgz and aseg_posterior.mgz, to split the
>amygdala by the plane z =27 on some particular brain, by some particular
>protocol).
>2. Edit  aseg_posterior.mgz (e.g. by tkmedit) to remove all amygdala
>anterior to z = 27. Similarly edit aseg_anterior.mgz to remove posterior
>segments.
>3. Run the stats on these edited segmentations, and record the data in
>aseg_posterior.stats and aseg_anterior.stats
>
> Does this sound reasonable and wise procedure? If so, is there a quick way
> to remove the unwanted segmentations without manually using a brush, slice
> by slice in tkmedit? Loading it into Matlab, like Doug suggests, would
> allow the edits I think, but then I'd have to rewrite the file from
> matlab.. I think.
>
> Josh
>
>
>
>
>
>
> On Wed, Nov 30, 2011 at 2:49 PM, Bruce Fischl 
> wrote:
>
>> yes
>>
>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>
>>  Actually, I have one last-last question.
>>> If I use mri_binarize on my aseg.mgz file, does it remain in the same
>>> 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz,
>>> will
>>> that z -coordinate still be valid in nifti file i'd have mri-Binarize
>>> create?
>>>
>>> Josh
>>>
>>>
>>> On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee  wrote:
>>>  I'm glad you caught that because I suddenly got really confused!
>>>  Thank Bruce for all your hard work!
>>>  Josh
>>>  -
>>>
>>>
>>> On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl
>>>  wrote:
>>>  oops, I meant the aseg.stats, not the aseg.mgz
>>>
>>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>>
>>>  Hi Bruce,
>>>
>>>  I'll see if I can phrase this right
>>>
>>>  In aseg.mgz each region has essentially been given a
>>>  unique number (e.g. 17
>>>  for left hippocampus, for example). ROI taken from
>>>  aseg.mgz volumes are
>>>  non-probabilistic, yes-no affairs already.
>>>  MRI_binarize just pulls this out
>>>  when we want to look at particular regions, say left
>>>  hipp???
>>>
>>>  Josh
>>>
>>>
>>>
>>>
>>>  On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl
>>>  
>>>  wrote:
>>>   probably not, as the aseg.stats calculation
>>>  uses partial volume
>>>   estimates.
>>>
>>>   cheers
>>>   Bruce
>>>
>>>  On Wed, 30 Nov 2011, Joshua Lee wrote:
>>>
>>>   Hey Doug, THanks. That looks simpler. I'll
>>>  probably use
>>>   that.
>>>
>>>   Question: Will the total volume of a ROI taken
>>>  from
>>>   aseg.mgz correspond to
>>>   the volume given in aseg.stats?
>>>
>>>   Josh
>>>
>>>
>>>
>>>   On Wed, Nov 30, 2011 at 9:55 AM, Douglas N
>>>  Greve
>>>   
>>>   wrote:
>>>If you have matlab, you can load the aseg
>>>  into
>>>   matlab, like
>>>aseg = MRIread('aseg.mgz');
>>>vol = length(aseg.vol(:,:,n:256) == ID);
>>>where ID is the code number for the ROI
>>>  you want  as
>>>   found in
>>>$FREESURFER_HOME/**FreeSurferColorLUT.txt
>>>doug
>>>
>>>Joshua Lee wrote:
>>>   Hi All,
>>>
>>>   I would like to determine the volumes of a
>>>  segmented
&g

Re: [Freesurfer] Error: [Cannot allocate memory] having 16GB of Memory.

[Joshua Lee]

I hear that PAE means that while your kernel is 32-bit it is configured to
use extended physical addresses so that the OS can use all your physical
memory. However,  PAE has a limitation: no single application can use more
than 4Gb of memory.

This is likely causing your crash. (BTW that is a lot of memory for one
recon-all process to ever reach...)

To solve this, you need to get a 64 bit installation, or find a way to stop
MRIalloc from needing so much memory.

Best of luck

Joshua


-
Joshua Lee
Center for Mind and Brain &
Department of Psychology
University of California, Davis



On Fri, Dec 2, 2011 at 7:21 AM, Fidel  wrote:

> Dear all,
>
> I'm having a problem running trac-all -prep.
> I receive this error (FROM THE TRAC-ALL.LOG WHICH IS ATTACHED):
>
> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 25th slice
>
> Cannot allocate memory
>
> Linux ubuntu 2.6.38-13-generic-pae #52-Ubuntu SMP Tue Nov 8 17:50:45 UTC
> 2011 i686 i686 i386 GNU/Linux
>
> trac-preproc exited with ERRORS at Fri Dec  2 05:02:57 PST 2011
>
> I am using Ubuntu 11.04 (Natty) 32bits and the kernel is
>  2.6.38-13-generic-pae, that is, it can use more than 4 GB of RAM (In fact,
> I was running it with 16GB of RAM) so we think memory was not the real
>  cause of the problem.
>
> The freesurfer version was: freesurfer-Linux-centos4-**stable-pub-v5.1.0
>
> Thanks and best regards.
>
> Fidel.
>
>
> ___
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>
>
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> 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.
>
>
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[Freesurfer] Entorhinal Labels and labels generally

[Joshua Lee]

I'm relatively new to Freesurfer, and have mostly focused of the aseg.mgz
segmentation. However, I am also interested in entorhinal cortex and loaded
the label up in tkmedit. What I noticed was that it seemed each label
essentially noted the border between white and gray matter, but didn't
really cover all the gray matter...this seems to be true in all the labels
I load in tkmedit.

In sum,  I don't really know what labels are for, or how they differ from
segmentations (is a segmentation a collection of labels?).
How do I use the entorhinal label, and do the entorhinal-stats actually
give the gray matter thickness despite appearing only as a border in
tkmedit. I'm afraid I'm quite ignorant, and I can't seem to find a direct
answer to them in the wiki.

Thanks,
Joshua
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Re: [Freesurfer] hippocampal subfields segmentation

[Joshua Lee]

I am not an expert but I'll say this as far as compliance to Duvernoy: In
the body of the hippocampus, compliance to Duvernoy is quite strongmuch
better than any others I've seen. However, according to my reading of
Duvernoy, the positions of the subfields change in the anterior head and
posterior tail, as compared to the body. Subiculum comes farther laterally,
and CA1 is further up superior-lateral (about at 10:00 o'clock), and
proceeds superiorally of the hippocmapus almost to the most medial extent
of the hippocampus...leading me to conclude that CA3 is very small in the
head, and may be non existent in the most anterior half of the headat
least according to my reading of Duvernoy atlas.

I want to reiterate my support for this project. The hippocampal subfields
are very important to a great number of researchers, as are the other MTL
structures (i.e. perirhinal cortex, posterior parahippocampal gyrus,
entorhinal cortex). By implementing an easy to use automated technique,
Freesurfer will, in my estimation become the de-facto standard in the
field. As such, I believe the segmentation protocol will come under
increased scrutiny by the community...and I wish that an effort is made by
someone (like Duvernoy but more robustly quantified) to create a standard
that is well validated by which all researchers may begin making
comparisons of their findings. The current Freesurfer implementation does a
pretty good job...but the field needs to come to terms with the positions
of the fields, and how those might change along the long-axis of the
hippocampus.

Best,

Joshua


n Thu, Jan 26, 2012 at 8:50 AM, Joana Braga Pereira  wrote:

> Dear Koen,
>
> Thanks! I will wait for Dr. Augustinack and Dr. Dickerson's answers.
>
> joana
>
>
> 2012/1/26 Koen Van Leemput 
>
>> Hi Joana,
>>
>> The smallness of our CA1 compared to other protocols seems to be
>> caused by disagreements in the fields of where the subfield boundaries
>> should be located. I've talked to several experts on this and they all
>> are confident that their own definition is the only "right" one. :-)
>>
>> As for the atlas our manual segmentations are based on, I believe it's
>> Duvernoy but I'm cc-ing Jean Augustinack and Brad Dickerson who know
>> more about this.
>>
>> Hope this helps,
>>
>> Koen
>>
>>
>> On Thu, Jan 26, 2012 at 9:54 AM, JOANA BRAGA PEREIRA
>>  wrote:
>> > Dear Koen & Freesurfers,
>> >
>> > I've been working with the GEMS tool for hippocampal subfields
>> > segmentation and have a question I would like to ask you all.
>> >
>> > I've noticed that the CA1 sector appears to be quite small compared to
>> > other subfields (CA2-3 seems to be the largest), while previous
>> > studies suggest that it should be the largest subfield of the
>> > hippocampus. Why?
>> >
>> > On the other hand, I have read the paper by Van Leemput et al. [2009]
>> > and how the subfields were initially delineated and was wondering what
>> > atlas was the manual tracing based on?
>> >
>> > Many thanks!
>> >
>> > joana
>> >
>> >
>> > ___
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>> >
>> >
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[Freesurfer] Hippocampal-subfields to ROI

[Joshua Lee]

Hi All,

I am wanting to run a functional analysis in spm using the hippo-subfields
as individual roi's. Thus I need to convert into a binary mask that is in
SPM space.
Knowing that the sub-field segmentations are probabilities [0..255] I chose
a threshold (i.e. ~95% certainty, corresponding to a value of ~240) and ran
mri_binarize with a min set at 240. However, the resultant image doesn't
retain the same dimensions as say brain.mgz, and appears as a black square
when overlayed. I suspect this will not work as a mask for roi analysis.
Any suggestions?

Thanks

Josh
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Re: [Freesurfer] Hippocampal subfield: average standard T1 ore use higher resolution

[Joshua Lee]

I think many have better scans than 1mm. Right now I'm using 0.7mm iso with
decent snr, and am collecting 2 scans (about 7 min each), and on most
slices I can see internal structural detail. It does seem a shame that all
this detail is not used for hippo-subfield segmentation.
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Tue, Feb 7, 2012 at 11:38 AM, Koen Van Leemput
wrote:

> Hi Oliver,
>
> You're right: internally we're upsampling the images to 0.5mm
> isotropic resolution, so if you had acquired 0.5mm isotropic images
> from the start, that would actually be much better (provided you don't
> simply trade off SNR for increased image matrix size). The catch with
> this is that the scripts I put in FreeSurfer will only work out of the
> box on FreeSurfer-reformatted 1mm resolution, so you'd need to tweak
> things a bit to get it working.
>
> Hope this helps,
>
> Koen
>
>
>
> On Thu, Feb 2, 2012 at 3:46 AM, Grimm, Oliver
>  wrote:
> >
> >
> > Dear FreeSurfer-User,
> >
> >
> >
> > some of my questions are mentioned in some older postings, but I still
> > struggle with some basic questions. We are planning to use the new
> > hippocampal subfield segmentation of FS 5.1 with 3 T Siemens TRIO with 32
> > channel head coil. Still, I do not fully understand how to optimize our
> > image processeing pipeline:
> >
> > Freesurfer works internally with 1x1x1 mm3 but the hippocampal segmenat
> uses
> > a higher res. of 0.5 x 0.5 x 0.5 mm3. So should we instead use a higher
> > resolution for the hippocampal subfield seg.?
> > I understand that the recent FS version is not working well with high
> > resolution images, e.g. the atlases are not provided in a higher res,
> > however the hippocampal subfield segmentation seems to make use of
> > aseg.stats. So is is possible at all to use the FS-pipleine in this case
> > (hippocampal subfields)?
> > Instead of using a high resolution image, we could average over several
> > pictures. When I tried this, I had the visual impression, that there was
> > almost no gain in this, the volume estimates were bouncing within a
> range of
> > 10% but did not converge when averaging from scan 1-5 to a specific
> value.
> > So is it necessary for a good quality to average images when using
> > hippocampal subfield segmentation ?
> >
> > Thanks for your efforts!
> >
> > Best,
> >
> >
> >
> >
> >
> > Dr. med. Oliver Grimm
> > Zentralinstitut für Seelische Gesundheit
> >
> > www.zi-mannheim.de
> >
> > SNiP | Systems Neuroscience in Psychiatry
> >
> > 68159 Mannheim
> >
> > Germany
> >
> >
> >
> > Tel: +49-621-1703-6341
> > Fax:+49-621-1703-6305
> > email oliver.gr...@zi-mannheim.de
> >
> >
> > ___
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> >
> >
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[Freesurfer] Question about hippocampal-subfield probability map

[Joshua Lee]

Dear experts,

The hippocampal-subfield are expressed as probability maps. For each
subfield, each voxel is assigned a probability of inclusion on a scale of
[0-255]=[0-1]. However, If I were to select only voxels from each
subfield's probability map corresponding to a >50% chance (i.e.
mri_binarize -min 150), then I would expect that no subfield would overlap
with another (i.e. a voxel shouldn't have greater than 50% probability of
belonging CA1, AND a greater than 50% probability of belonging to CA4-DG.
However it appears that this is not the case, and overlap does occur. Thus,
unless I messed up, subfields are not mutually exclusive. Have I got this
right? And if so, how do I obtain binary maps of subfields with no overlap?

Thanks

Josh
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Re: [Freesurfer] Question about hippocampal-subfield probability map

[Joshua Lee]

Ha nevermind. While true, I can just mask the masks with each other and
drop the over lapped regions.
-
Josh


On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee  wrote:

> Dear experts,
>
> The hippocampal-subfield are expressed as probability maps. For each
> subfield, each voxel is assigned a probability of inclusion on a scale of
> [0-255]=[0-1]. However, If I were to select only voxels from each
> subfield's probability map corresponding to a >50% chance (i.e.
> mri_binarize -min 150), then I would expect that no subfield would overlap
> with another (i.e. a voxel shouldn't have greater than 50% probability of
> belonging CA1, AND a greater than 50% probability of belonging to CA4-DG.
> However it appears that this is not the case, and overlap does occur. Thus,
> unless I messed up, subfields are not mutually exclusive. Have I got this
> right? And if so, how do I obtain binary maps of subfields with no overlap?
>
> Thanks
>
> Josh
>
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Re: [Freesurfer] Question about hippocampal-subfield probability map

[Joshua Lee]

That is, I can use fslmaths from fsl suite to subtract my binarized
subfield rois.
-
Josh


On Tue, Feb 14, 2012 at 4:58 PM, Joshua Lee  wrote:

> Ha nevermind. While true, I can just mask the masks with each other and
> drop the over lapped regions.
> -
> Josh
>
>
> On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee  wrote:
>
>> Dear experts,
>>
>> The hippocampal-subfield are expressed as probability maps. For each
>> subfield, each voxel is assigned a probability of inclusion on a scale of
>> [0-255]=[0-1]. However, If I were to select only voxels from each
>> subfield's probability map corresponding to a >50% chance (i.e.
>> mri_binarize -min 150), then I would expect that no subfield would overlap
>> with another (i.e. a voxel shouldn't have greater than 50% probability of
>> belonging CA1, AND a greater than 50% probability of belonging to CA4-DG.
>> However it appears that this is not the case, and overlap does occur. Thus,
>> unless I messed up, subfields are not mutually exclusive. Have I got this
>> right? And if so, how do I obtain binary maps of subfields with no overlap?
>>
>> Thanks
>>
>> Josh
>>
>
>
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[Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

[Joshua Lee]

Hi All,

I thought I'd share my recent experiences with the newest Freesurfer v.
5.10 and subcortical segmentation.

I ran a large sample of brains using the default stream of Freesurfer v.
5.10. The resulting hippocampal segmentations were extremely poor, yet on
the same sample of brains Freesurfer v. 4.xx did quite well.

Using tkregister, we discovered that the hippocampus is not being
registered well enough. Nick Schmansky one wrote in another post on this
list-serve that one difference between versions is that "talairach.xfm is
needed to compute nu.mgz, [and] talairach stage needs to precede the
nu_correct stage" He suggested using -use-mritotal in the recon-all command
to overcome tal-check failures.

I decided to try using -use-mritotal with this sample of my data, despite
tal-check not failing in the default stream. Resulting segmentations were
now both realistic and accurate, and near identical to those produced by
Freesurfer version 4.xx.

Have others experienced poor subcortical segmentation with current version
of Freesurfer? I should note, that I am having this problem on another
sample of MPRages of very good quality. I am concerned that future versions
of Freesurfer will limit use of the old stream to situations in which
tal-check fails.

Thanks you all.
 Sincerely,

Joshua Lee
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Re: [Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

[Joshua Lee]

It was version 4.50. I had to walk over to the other room to find out. ;)

 In any case, I achieved good results by including the use-mritotal flag on
the current version.

Josh



On Tue, Apr 17, 2012 at 12:00 PM, Alan Francis wrote:

> Hi Joshua:
>
> What version of FS 4 did you use?
>
> best,
>
> Alan
>
> On Tue, Apr 17, 2012 at 2:56 PM, Joshua Lee  wrote:
>
>> Hi All,
>>
>> I thought I'd share my recent experiences with the newest Freesurfer v.
>> 5.10 and subcortical segmentation.
>>
>> I ran a large sample of brains using the default stream of Freesurfer v.
>> 5.10. The resulting hippocampal segmentations were extremely poor, yet on
>> the same sample of brains Freesurfer v. 4.xx did quite well.
>>
>> Using tkregister, we discovered that the hippocampus is not being
>> registered well enough. Nick Schmansky one wrote in another post on this
>> list-serve that one difference between versions is that "talairach.xfm
>> is needed to compute nu.mgz, [and] talairach stage needs to precede the
>> nu_correct stage" He suggested using -use-mritotal in the recon-all command
>> to overcome tal-check failures.
>>
>> I decided to try using -use-mritotal with this sample of my data, despite
>> tal-check not failing in the default stream. Resulting segmentations were
>> now both realistic and accurate, and near identical to those produced by
>> Freesurfer version 4.xx.
>>
>> Have others experienced poor subcortical segmentation with current
>> version of Freesurfer? I should note, that I am having this problem on
>> another sample of MPRages of very good quality. I am concerned that future
>> versions of Freesurfer will limit use of the old stream to situations in
>> which tal-check fails.
>>
>> Thanks you all.
>>  Sincerely,
>>
>> Joshua Lee
>>
>>
>> ___
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
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>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
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Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

[Joshua Lee]

I was told to use this recon-all flag and my talairach problem went away:
-use-mritotal
-
Josh

On Tue, Apr 17, 2012 at 7:51 AM, Nick Schmansky
wrote:

> Ed,
>
> email probably trounced it.  recon-all is a text file.  attached is a
> gzipped version.  use gunzip to unpack it.
>
> N.
>
>
>
> On Tue, 2012-04-17 at 16:45 +0200, Ed Gronenschild wrote:
> > Hi Nick,
> >
> > It does not work properly, it only produces an error message,
> > even with no option at all:
> >
> > 'nknown option: '-
> > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ...].
> >
> > Ed
> >
> > On 17 Apr 2012, at 16:28, Nick Schmansky wrote:
> >
> > > a modified recon-all is attached.  it will run nu_correct prior to the
> > > talairach stage, as will be the case with v5.2.  so you can just run:
> > >
> > > recon-all -s subjid -all -clean-tal
> > >
> > > n.
> > >
> > >
> > > On Tue, 2012-04-17 at 08:58 +0200, Ed Gronenschild wrote:
> > >> Hi Nick,
> > >>
> > >> The option -talairach-nu is not recognized in version v5.1.0.
> > >>
> > >> How can I proceed now?
> > >>
> > >> Ed
> > >>
> > >> On 16 Apr 2012, at 17:32, Nick Schmansky wrote:
> > >>
> > >>> Ed,
> > >>>
> > >>> Hi, no there is not an option to switch them.  The nu correct
> > >>> stage in
> > >>> 5.1 needs the talairach to run.
> > >>>
> > >>> However, if your intent is to get a better talairach result by
> > >>> using the
> > >>> nu corrected input (as it did prior to v5.1), then you can do the
> > >>> following:
> > >>>
> > >>> recon-all -s subjid -motioncor -talairach -nuintensitycor
> > >>>
> > >>> then run:
> > >>>
> > >>> recon-all -s subjid -all -talairach-nu -clean-tal
> > >>>
> > >>> on the second run, it will use the nu.mgz in the talairach stage.
> > >>>
> > >>> Note that in the next version, v5.2, one iteration of nu_correct
> > >>> will be
> > >>> run prior to the talairach stage to use as input to the talairach
> > >>> stage,
> > >>> in order to get the better talairach results that people were seeing
> > >>> prior to v5.1.  it will still run the current nu_correct stage to
> > >>> create
> > >>> nu.mgz (the nu used in talairach gets discarded).
> > >>>
> > >>> Nick
> > >>>
> > >>>
> > >>>
> > >>> On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote:
> >  Hi,
> > 
> >  As of version 5.1 the Talairach stage precedes the nu-correction
> >  stage.
> >  Is there an option or possibility to switch this order?
> > 
> >  Cheers,
> >  Ed
> >  ___
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> > 
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> 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
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> > >>> contains patient information, please contact the Partners
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> > >>
> > >>
> > >
> > > 
> >
> >
>
>
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Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

[Joshua Lee]

wait it was Nick that told me to use this a while back when I had tal-check
failures...I just posted about my current issues where I discuss my recent
experiences with a high rate of talairach failures in the current version.
-
Josh


On Tue, Apr 17, 2012 at 12:49 PM, Joshua Lee  wrote:

> I was told to use this recon-all flag and my talairach problem went away:
> -use-mritotal
> -
> Josh
>
> On Tue, Apr 17, 2012 at 7:51 AM, Nick Schmansky  > wrote:
>
>> Ed,
>>
>> email probably trounced it.  recon-all is a text file.  attached is a
>> gzipped version.  use gunzip to unpack it.
>>
>> N.
>>
>>
>>
>> On Tue, 2012-04-17 at 16:45 +0200, Ed Gronenschild wrote:
>> > Hi Nick,
>> >
>> > It does not work properly, it only produces an error message,
>> > even with no option at all:
>> >
>> > 'nknown option: '-
>> > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ...].
>> >
>> > Ed
>> >
>> > On 17 Apr 2012, at 16:28, Nick Schmansky wrote:
>> >
>> > > a modified recon-all is attached.  it will run nu_correct prior to the
>> > > talairach stage, as will be the case with v5.2.  so you can just run:
>> > >
>> > > recon-all -s subjid -all -clean-tal
>> > >
>> > > n.
>> > >
>> > >
>> > > On Tue, 2012-04-17 at 08:58 +0200, Ed Gronenschild wrote:
>> > >> Hi Nick,
>> > >>
>> > >> The option -talairach-nu is not recognized in version v5.1.0.
>> > >>
>> > >> How can I proceed now?
>> > >>
>> > >> Ed
>> > >>
>> > >> On 16 Apr 2012, at 17:32, Nick Schmansky wrote:
>> > >>
>> > >>> Ed,
>> > >>>
>> > >>> Hi, no there is not an option to switch them.  The nu correct
>> > >>> stage in
>> > >>> 5.1 needs the talairach to run.
>> > >>>
>> > >>> However, if your intent is to get a better talairach result by
>> > >>> using the
>> > >>> nu corrected input (as it did prior to v5.1), then you can do the
>> > >>> following:
>> > >>>
>> > >>> recon-all -s subjid -motioncor -talairach -nuintensitycor
>> > >>>
>> > >>> then run:
>> > >>>
>> > >>> recon-all -s subjid -all -talairach-nu -clean-tal
>> > >>>
>> > >>> on the second run, it will use the nu.mgz in the talairach stage.
>> > >>>
>> > >>> Note that in the next version, v5.2, one iteration of nu_correct
>> > >>> will be
>> > >>> run prior to the talairach stage to use as input to the talairach
>> > >>> stage,
>> > >>> in order to get the better talairach results that people were seeing
>> > >>> prior to v5.1.  it will still run the current nu_correct stage to
>> > >>> create
>> > >>> nu.mgz (the nu used in talairach gets discarded).
>> > >>>
>> > >>> Nick
>> > >>>
>> > >>>
>> > >>>
>> > >>> On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote:
>> > >>>> Hi,
>> > >>>>
>> > >>>> As of version 5.1 the Talairach stage precedes the nu-correction
>> > >>>> stage.
>> > >>>> Is there an option or possibility to switch this order?
>> > >>>>
>> > >>>> Cheers,
>> > >>>> Ed
>> > >>>> ___
>> > >>>> 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.
>> > >>
>> > >>
>> > >
>> > > 
>> >
>> >
>>
>>
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>> is
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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
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Re: [Freesurfer] -use-mritotal

[Joshua Lee]

Hi Steven,

It has been recommended to me that in case of Tal-check failures, the
use of the -use-mritotal flag will overcome this issue. However, this
substitutes Freesurfer's registration algorithms with a function from
MNI, I believe. In general, I have heard it said that mritotal does a
poorer job, than the freesurfer implementation, thus this may not be
the best option.

In the current version of Freesurfer, as I have been told,
talairach.xfm is needed to compute nu.mgz, [and] talairach stage needs
to precede the nu_correct stage. In my data set, this has led to
poorer registration, and hippocampal segmentations.

At first, I resolved to use mritotal which helped things somewhat.
However, on a recent thread on the list-serve, a modified recon-all
script file was posted by Nick Schmansky that resolves this issue. In
the script are some changes that will be put into the next version
release of Freesurfer, one of which resolves the talairach issue. I
downloaded the script, and replaced the 5.1 version of the recon-all
script. You will find the recon-all script in a message entitled:

[Freesurfer] How to switch order of Talairach and nu-correction stages
in recon-all

As I mentioned, this new recon-all file resolved my issue with poor
hippocampal segmentations


-
Joshua Lee



On Thu, Apr 19, 2012 at 8:51 AM, Steven Korycinski  wrote:
>
> Hi all,
>
> I've been following an e-mail on this list-serve from Joshua Lee
> regarding poor hippocampal segmentations in Freesurfer 5.1. He
> mentions "using -use-mritotal in the recon-all command to overcome
> tal-check failures" to help fix the segmentation and make them more
> like "those produced by Freesurfer version 4.xx." In light of this
> information, would you recommend that all normal Freesurfer 5.1 users
> add this flag to the recon-all command to help with any segmentation
> errors? Also, at what stage(s) in the reconstruction process should
> the flag be included (ie. recon-all -autorecon1,2, or 3)?
>
> Thanks,
>
> Steve
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> at
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