[Freesurfer] Upgrading Software

[joseph veliz]

Hello,


Is there any detailed information on the possible differences in results
wwhen upgrading to the latest FreeSurfer software?

As it pertains to the scans already processed with old software compared to
any scans processed with a newer version of the software.

Can I install the new version of Freeview without the new version of
FreeSurfer? Would there be any differences to between scans corrected
before and after upgrade?

I cannot seem to get the 'curl -O' to download the software. Are there any
troubleshooting methods to this? Testing the harvard ftp server also fails.
Has it been down?

Thank you so much,

Joseph
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[Freesurfer] Versions compatibility

[joseph veliz]

Hello,

We are running on

Mac OSX 10.6.8

X11 version 2.3.6

Reading the download page recommends Xquarts 2.7.5 for 10.7

How important is the X11 requirment?

At this point (80 subjects freesurfed), is it recommended to update X11?

I warned about not upgrading operating system between studies, correct?
Wondering if this X11 also applies to that general rule.

Thanks so much

Joseph
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[Freesurfer] darker user interface

[joseph veliz]

Hello,

Is there any way to have a black background / white font foreground for the
user interface on Freeveiw?


I am working in a dark reading room with others at times and the white user
interface reflects on other screens.


I noticed a dark mode for the command console on the preferences but it
doesn't seem to work.


thanks

Joseph
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[Freesurfer] Freeview Update

[joseph veliz]

Hello,

I am running freesurfer  darwin leopard i686 v5.1.0 and am trying to update
to the latest freeview.

Following the download/installation instructions by deleting the
freeview.app file from the application folder and replacing it with the new
freeview.app file, does not seem to work.

Applications/freesurfer/bin/freeview.app is the only location I can  find
the freeview.app.

After replacing freeview.app file.

When calling freeview on terminal, error;
"/Applications/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin:
Command not found."

What am I doing wrong?







A second issue,

I would like to use another macbook to freeview - edit data created by
freesurfer recons by another iMac

and then transfer the macbook edited data back to the iMac to do the re
re-cons.


Would there be any issues with this plan ?



Thanks so much

Joseph
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Re: [Freesurfer] Freeview Update

[joseph veliz]

Thanks Zeke,


Could you please help me understand if there would be any inconsistencies
or variation between data sets edited by Freeview on a newer macbook pro vs
data sets edited by Freeview on a older iMac?

I want to make corrections using latest Freeview update on a new macbook
pro.

Is Freeview a stand alone application?
Could I install Freeview and use it to edit, without prior installation of
Freesurfer?

Can I transfer the edited data to another (older) iMac that has older
version of Freesurfer and maintain a consistent data set across subjects?

I have a data set of 100 subjects that have been re-con all on a iMac (
Freesurfer 5.1.0). I am concerned about editing those subjects on a newer
macbook pro with a new version of Freeview.

Any thoughts on my hesitation to do so?

Thank so much again,

Joseph Veliz



On Thu, Jun 18, 2015 at 7:35 PM, Z K  wrote:

> The instructions for updating freeview only work when updating from the
> most recent freesurfer release (i.e. version 5.3). It won't work if
> updating from version 5.1
>
> If you want to use the latest development version of freeview you will
> have to update to the most recent version of freesurfer, then apply the
> update.
>
> -Zeke
>
>
> > On Jun 18, 2015, at 11:04 AM, joseph veliz 
> wrote:
> >
> > Hello,
> >
> > I am running freesurfer  darwin leopard i686 v5.1.0 and am trying to
> update to the latest freeview.
> >
> > Following the download/installation instructions by deleting the
> freeview.app file from the application folder and replacing it with the new
> freeview.app file, does not seem to work.
> >
> > Applications/freesurfer/bin/freeview.app is the only location I can
> find the freeview.app.
> >
> > After replacing freeview.app file.
> >
> > When calling freeview on terminal, error;
> "/Applications/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin:
> Command not found."
> >
> > What am I doing wrong?
> >
> >
> >
> >
> >
> >
> >
> > A second issue,
> >
> > I would like to use another macbook to freeview - edit data created by
> freesurfer recons by another iMac
> >
> > and then transfer the macbook edited data back to the iMac to do the re
> re-cons.
> >
> >
> > Would there be any issues with this plan ?
> >
> >
> >
> > Thanks so much
> >
> > Joseph
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

[joseph veliz]

Hello,


We are having issues installing Freeview on Macbook pro (2015)

2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris pro graphic
processing.

Installing lastest Freesurfer and Freeview downloads of Darwin lion v5.3.0.

After installing Freesurfer , license and environment setup, the only
freeview found is in the bin folder and is named freeview.bin

Commands to open freeview did not work.

Then I placed the seperately downloaded Freeview.app in the
/application/freesurfer directory, then the command freeview responded.

We don't know if we are putting the Freeview.app in the correct directory?

When opening freeview;

Volumes are loading fine, but when a Surface is loaded the program quits,
giving error message.

I am thinking the integrated graphics could be the issue (uses computers
RAM). Reading the freesurfer Requirments wiki,
Graphics card: 3D graphics card with its own graphics memory & accelerated
OpenGL drivers. Could this be the issue even though the macbook has 16GB
DDR3 to spare?

Also I don't think I am placing the Freeview.app in the correct directory?

Both gui and script attempts fail loading Surfaces and return error

2015-06-23 12:43:29.660 Freeview[1855:303] modalSession has been exited
prematurely - check for a reentrant call to endModalSession:
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

[0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 5 TRAP
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:

[0]PETSC ERROR: Unknown Name on a darwin12. named fmris-MacBook-Pro.local
by Dopamine Tue Jun 23 12:40:59 2015
[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:

[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0



Any help or comments are much appreciated

Thank you so much,

Jospeh Veliz
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Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

[joseph veliz]

Positive we downloaded Freesurfer -Darwin - lion -dev.tar.gz

On Thu, Jun 25, 2015 at 9:04 AM, Z K  wrote:

>
>
> On 06/23/2015 04:52 PM, joseph veliz wrote:
> > Hello,
> >
> >
> > We are having issues installing Freeview on Macbook pro (2015)
> >
> > 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris pro graphic
> > processing.
> >
> > Installing lastest Freesurfer and Freeview downloads of Darwin lion
> v5.3.0.
> >
> > After installing Freesurfer , license and environment setup, the only
> > freeview found is in the bin folder and is named freeview.bin
>
> This doenst make sense because the OSX distribution of freesurfer does
> not contain a "freeview.bin" file. Only the linux distribution contains
> that file. Are you sure you didn't download and install the linux build
> on your OSX machine?
>
>
> -Zeke
>
>
> >
> > Commands to open freeview did not work.
> >
> > Then I placed the seperately downloaded Freeview.app in the
> > /application/freesurfer directory, then the command freeview responded.
> >
> > We don't know if we are putting the Freeview.app in the correct
> directory?
> >
> > When opening freeview;
> >
> > Volumes are loading fine, but when a Surface is loaded the program
> > quits, giving error message.
> >
> > I am thinking the integrated graphics could be the issue (uses computers
> > RAM). Reading the freesurfer Requirments wiki,
> > Graphics card: 3D graphics card with its own graphics memory &
> > accelerated OpenGL drivers. Could this be the issue even though the
> > macbook has 16GB DDR3 to spare?
> >
> > Also I don't think I am placing the Freeview.app in the correct
> directory?
> >
> > Both gui and script attempts fail loading Surfaces and return error
> >
> > 2015-06-23 12:43:29.660 Freeview[1855:303] modalSession has been exited
> > prematurely - check for a reentrant call to endModalSession:
> > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
> >Referenced from:
> >
> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
> >Expected in: /usr/lib/libSystem.B.dylib
> >
> > dyld: Symbol not found: ___emutls_get_address
> >Referenced from:
> >
> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
> >Expected in: /usr/lib/libSystem.B.dylib
> >
> > [0]PETSC ERROR:
> > 
> > [0]PETSC ERROR: Caught signal number 5 TRAP
> > [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > [0]PETSC ERROR: or see
> >
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> > ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> > find memory corruption errors
> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> > and run
> > [0]PETSC ERROR: to get more information on the crash.
> > [0]PETSC ERROR: - Error Message
> > 
> > [0]PETSC ERROR: Signal received!
> > [0]PETSC ERROR:
> > 
> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
> > 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR:
> > 
> > [0]PETSC ERROR: Unknown Name on a darwin12. named
> > fmris-MacBook-Pro.local by Dopamine Tue Jun 23 12:40:59 2015
> > [0]PETSC ERROR: Libraries linked from
> >
> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
> > [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
> > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> > --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> > --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> > [0]PETSC ERROR:
> > 
> > [0]PETSC ERROR: User provided function() line 0 in unknown directory
> > unknown file
> > [unset]: aborting job:
> > application c

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

[joseph veliz]

Sorry that is an archive zip that i also downloaded

The one installed is Freesurfer -Darwin -lion -stabel -pub-v5.3.0.dmg



On Thu, Jun 25, 2015 at 10:36 AM, joseph veliz 
wrote:

> Positive we downloaded Freesurfer -Darwin - lion -dev.tar.gz
>
> On Thu, Jun 25, 2015 at 9:04 AM, Z K  wrote:
>
>>
>>
>> On 06/23/2015 04:52 PM, joseph veliz wrote:
>> > Hello,
>> >
>> >
>> > We are having issues installing Freeview on Macbook pro (2015)
>> >
>> > 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris pro graphic
>> > processing.
>> >
>> > Installing lastest Freesurfer and Freeview downloads of Darwin lion
>> v5.3.0.
>> >
>> > After installing Freesurfer , license and environment setup, the only
>> > freeview found is in the bin folder and is named freeview.bin
>>
>> This doenst make sense because the OSX distribution of freesurfer does
>> not contain a "freeview.bin" file. Only the linux distribution contains
>> that file. Are you sure you didn't download and install the linux build
>> on your OSX machine?
>>
>>
>> -Zeke
>>
>>
>> >
>> > Commands to open freeview did not work.
>> >
>> > Then I placed the seperately downloaded Freeview.app in the
>> > /application/freesurfer directory, then the command freeview responded.
>> >
>> > We don't know if we are putting the Freeview.app in the correct
>> directory?
>> >
>> > When opening freeview;
>> >
>> > Volumes are loading fine, but when a Surface is loaded the program
>> > quits, giving error message.
>> >
>> > I am thinking the integrated graphics could be the issue (uses computers
>> > RAM). Reading the freesurfer Requirments wiki,
>> > Graphics card: 3D graphics card with its own graphics memory &
>> > accelerated OpenGL drivers. Could this be the issue even though the
>> > macbook has 16GB DDR3 to spare?
>> >
>> > Also I don't think I am placing the Freeview.app in the correct
>> directory?
>> >
>> > Both gui and script attempts fail loading Surfaces and return error
>> >
>> > 2015-06-23 12:43:29.660 Freeview[1855:303] modalSession has been exited
>> > prematurely - check for a reentrant call to endModalSession:
>> > dyld: lazy symbol binding failed: Symbol not found:
>> ___emutls_get_address
>> >Referenced from:
>> >
>> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>> >Expected in: /usr/lib/libSystem.B.dylib
>> >
>> > dyld: Symbol not found: ___emutls_get_address
>> >Referenced from:
>> >
>> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>> >Expected in: /usr/lib/libSystem.B.dylib
>> >
>> > [0]PETSC ERROR:
>> > 
>> > [0]PETSC ERROR: Caught signal number 5 TRAP
>> > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > [0]PETSC ERROR: or see
>> >
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> > ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple
>> to
>> > find memory corruption errors
>> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> > and run
>> > [0]PETSC ERROR: to get more information on the crash.
>> > [0]PETSC ERROR: - Error Message
>> > 
>> > [0]PETSC ERROR: Signal received!
>> > [0]PETSC ERROR:
>> > 
>> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
>> > 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> > [0]PETSC ERROR: See docs/index.html for manual pages.
>> > [0]PETSC ERROR:
>> > 
>> > [0]PETSC ERROR: Unknown Name on a darwin12. named
>> > fmris-MacBook-Pro.local by Dopamine Tue Jun 23 12:40:59 2015
>> > [0]PETSC ERROR: Libraries linked from
>> >
>> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
>> >

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

[joseph veliz]

sorry for the confusion

I assure it is the correct download installed

Looking at the file again it does not have a '.bin' , but it is in the bin
folder

and is very small file  184 bytes

the build-stamp.txt file say freesurfer-Darwin-lion-stable -pub-v5.3.0

On Thu, Jun 25, 2015 at 11:22 AM, Z K  wrote:

> Although I can confirm the issue with surface files. Please wait a day
> updating freeview. I will resolve the issue and email you and the list
> once it is resolved. Hopefully within the day.
>
> -Zeke
>
> On 06/25/2015 02:20 PM, Z K wrote:
> > H. Im not really sure how to proceed because you should not have
> > that file. What does your build-stamp.txt file contain? Twice I have
> > tested by downloading the lion OSX version of freesurfer from this page:
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Download
> >
> > and never was a file called "freeview.bin" part of the installation.
> > Perhaps you could consider completely removing the current installation
> > and re-install? making absolutely sure you are using
> > freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
> >
> > Once that is complete you can update to the newst freeview. Download the
> > following link
> > (
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview.zip
> ),
> > Double click it, and replace you $FREESURFER_HOME/Freeview file with the
> > one in the zip file.
> >
> > -Zeke
> >
> > On 06/25/2015 01:39 PM, joseph veliz wrote:
> >> Sorry that is an archive zip that i also downloaded
> >>
> >> The one installed is Freesurfer -Darwin -lion -stabel -pub-v5.3.0.dmg
> >>
> >>
> >>
> >> On Thu, Jun 25, 2015 at 10:36 AM, joseph veliz  >> <mailto:josephveli...@gmail.com>> wrote:
> >>
> >>  Positive we downloaded Freesurfer -Darwin - lion -dev.tar.gz
> >>
> >>  On Thu, Jun 25, 2015 at 9:04 AM, Z K  >>  <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote:
> >>
> >>
> >>
> >>  On 06/23/2015 04:52 PM, joseph veliz wrote:
> >>  > Hello,
> >>  >
> >>  >
> >>  > We are having issues installing Freeview on Macbook pro
> (2015)
> >>  >
> >>  > 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris
> pro graphic
> >>  > processing.
> >>  >
> >>  > Installing lastest Freesurfer and Freeview downloads of
> Darwin lion v5.3.0.
> >>  >
> >>  > After installing Freesurfer , license and environment setup,
> the only
> >>  > freeview found is in the bin folder and is named freeview.bin
> >>
> >>  This doenst make sense because the OSX distribution of
> >>  freesurfer does
> >>  not contain a "freeview.bin" file. Only the linux distribution
> >>  contains
> >>  that file. Are you sure you didn't download and install the
> >>  linux build
> >>  on your OSX machine?
> >>
> >>
> >>  -Zeke
> >>
> >>
> >>   >
> >>   > Commands to open freeview did not work.
> >>   >
> >>   > Then I placed the seperately downloaded Freeview.app in the
> >>   > /application/freesurfer directory, then the command freeview
> >>  responded.
> >>   >
> >>   > We don't know if we are putting the Freeview.app in the
> >>  correct directory?
> >>   >
> >>   > When opening freeview;
> >>   >
> >>   > Volumes are loading fine, but when a Surface is loaded the
> >>  program
> >>   > quits, giving error message.
> >>   >
> >>   > I am thinking the integrated graphics could be the issue
> >>  (uses computers
> >>   > RAM). Reading the freesurfer Requirments wiki,
> >>   > Graphics card: 3D graphics card with its own graphics
> memory &
> >>   > accelerated OpenGL drivers. Could this be the issue even
> >>  though the
> >>   > macbook has 16GB DDR3 to spare?
> >>   >
> >>   > Also I don't think I am placing the Freeview.app in the
> >>  correct directory?
> >> 

Re: [Freesurfer] [FreeSurfer] aparc+aseg.mgz unkown voxels

[joseph veliz]

leopard i686 stable pub v5.1.0

As an aside I watched your introductory videos and found you to be very
knowledgeable, well-spoken and very helpful in understanding some of the
amazing things you guys are doing for analysis. Really cool to be emailing
you and getting help from the pros.

Thanks

Joe

On Wed, Jul 1, 2015 at 1:12 PM, Bruce Fischl 
wrote:

> Hi Joe
>
> what FS version are you using? That certainly looks like a bug, but maybe
> it's one we've fixed already?
>
> Bruce
>
>
> On Wed, 1 Jul 2015, joseph veliz wrote:
>
> > Hello Freesrufers,
> >
> > There are voxels in random areas of the aparc+aseg.mgz that are
> categorized
> > as 'unknown'.
> >
> > I read an earlier email stating that aparc+aseg.mgz should not be
> directly
> > edited by filling in voxels. Correct?
> >
> > A specific example of this is shown on the attatched images.
> >
> > aseg.mgz categorizes this area as cortex, yet the aparc+aseg.mgz does not
> > even though it is within pial boundary and is adjacent to other
> > (categorized) cortical and sub cortical regions.
> >
> > How could we go about correcting this?
> >
> > Thank so much
> >
> > Joe
> >
> >
> ___
> 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] [FreeSurfer] aparc+aseg.mgz unkown voxels

[joseph veliz]

We have quite a large data set we have processed in this study on v5.1.0
and have been previously advised to not switch versions in-between
processing data sets.

I do have a macbook pro running v5.3, I will attempt to recon on this
subject.

But are there any other options on v5.1?

Why is it that voxels in aparc+aseg.mgz can not just be filled in with
corresponding color from the lut?



On Thu, Jul 2, 2015 at 6:04 AM, Douglas N Greve 
wrote:

> I think that might have been fixed in 5.3. Can you try 5.3 on that one
> subject to see? Thanks for the kudos.
> doug
>
> On 07/01/2015 08:23 PM, joseph veliz wrote:
> > leopard i686 stable pub v5.1.0
> >
> > As an aside I watched your introductory videos and found you to be
> > very knowledgeable, well-spoken and very helpful in understanding some
> > of the amazing things you guys are doing for analysis. Really cool to
> > be emailing you and getting help from the pros.
> >
> > Thanks
> >
> > Joe
> >
> > On Wed, Jul 1, 2015 at 1:12 PM, Bruce Fischl
> > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Joe
> >
> > what FS version are you using? That certainly looks like a bug,
> > but maybe
> > it's one we've fixed already?
> >
> > Bruce
> >
> >
> > On Wed, 1 Jul 2015, joseph veliz wrote:
> >
> > > Hello Freesrufers,
> > >
> > > There are voxels in random areas of the aparc+aseg.mgz that are
> > categorized
> > > as 'unknown'.
> > >
> > > I read an earlier email stating that aparc+aseg.mgz should not
> > be directly
> > > edited by filling in voxels. Correct?
> > >
> > > A specific example of this is shown on the attatched images.
> > >
> > > aseg.mgz categorizes this area as cortex, yet the aparc+aseg.mgz
> > does not
> > > even though it is within pial boundary and is adjacent to other
> > > (categorized) cortical and sub cortical regions.
> > >
> > > How could we go about correcting this?
> > >
> > > Thank so much
> > >
> > > Joe
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
>
> --
> 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
>
___
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Re: [Freesurfer] [FreeSurfer] aparc+aseg.mgz unkown voxels

[joseph veliz]

I have updated our macbook 10.9 with the latest freesurfer from;

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz


The same results are produced; ' unknown voxels ' on the aparc+aseg.mgz.

I am not sure how to proceed, are there any suggestions?

thank you so much

joseph




On Thu, Jul 2, 2015 at 12:45 PM, joseph veliz 
wrote:

> We have quite a large data set we have processed in this study on v5.1.0
> and have been previously advised to not switch versions in-between
> processing data sets.
>
> I do have a macbook pro running v5.3, I will attempt to recon on this
> subject.
>
> But are there any other options on v5.1?
>
> Why is it that voxels in aparc+aseg.mgz can not just be filled in with
> corresponding color from the lut?
>
>
>
> On Thu, Jul 2, 2015 at 6:04 AM, Douglas N Greve  > wrote:
>
>> I think that might have been fixed in 5.3. Can you try 5.3 on that one
>> subject to see? Thanks for the kudos.
>> doug
>>
>> On 07/01/2015 08:23 PM, joseph veliz wrote:
>> > leopard i686 stable pub v5.1.0
>> >
>> > As an aside I watched your introductory videos and found you to be
>> > very knowledgeable, well-spoken and very helpful in understanding some
>> > of the amazing things you guys are doing for analysis. Really cool to
>> > be emailing you and getting help from the pros.
>> >
>> > Thanks
>> >
>> > Joe
>> >
>> > On Wed, Jul 1, 2015 at 1:12 PM, Bruce Fischl
>> > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > Hi Joe
>> >
>> > what FS version are you using? That certainly looks like a bug,
>> > but maybe
>> > it's one we've fixed already?
>> >
>> > Bruce
>> >
>> >
>> > On Wed, 1 Jul 2015, joseph veliz wrote:
>> >
>> > > Hello Freesrufers,
>> > >
>> > > There are voxels in random areas of the aparc+aseg.mgz that are
>> > categorized
>> > > as 'unknown'.
>> > >
>> > > I read an earlier email stating that aparc+aseg.mgz should not
>> > be directly
>> > > edited by filling in voxels. Correct?
>> > >
>> > > A specific example of this is shown on the attatched images.
>> > >
>> > > aseg.mgz categorizes this area as cortex, yet the aparc+aseg.mgz
>> > does not
>> > > even though it is within pial boundary and is adjacent to other
>> > > (categorized) cortical and sub cortical regions.
>> > >
>> > > How could we go about correcting this?
>> > >
>> > > Thank so much
>> > >
>> > > Joe
>> > >
>> > >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu > 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
>>
>> --
>> 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
>>
>
>
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[Freesurfer] Fwd: [FreeSurfer] aparc+aseg.mgz unkown voxels

[joseph veliz]

Hello,

Just checking if this email thread was still being tracked.

Thanks so much

Joseph
-- Forwarded message --
From: joseph veliz 
Date: Thu, Jul 9, 2015 at 10:41 AM
Subject: Re: [Freesurfer] [FreeSurfer] aparc+aseg.mgz unkown voxels
To: Freesurfer support list 


I have updated our macbook 10.9 with the latest freesurfer from;

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz


The same results are produced; ' unknown voxels ' on the aparc+aseg.mgz.

I am not sure how to proceed, are there any suggestions?

thank you so much

joseph




On Thu, Jul 2, 2015 at 12:45 PM, joseph veliz 
wrote:

> We have quite a large data set we have processed in this study on v5.1.0
> and have been previously advised to not switch versions in-between
> processing data sets.
>
> I do have a macbook pro running v5.3, I will attempt to recon on this
> subject.
>
> But are there any other options on v5.1?
>
> Why is it that voxels in aparc+aseg.mgz can not just be filled in with
> corresponding color from the lut?
>
>
>
> On Thu, Jul 2, 2015 at 6:04 AM, Douglas N Greve  > wrote:
>
>> I think that might have been fixed in 5.3. Can you try 5.3 on that one
>> subject to see? Thanks for the kudos.
>> doug
>>
>> On 07/01/2015 08:23 PM, joseph veliz wrote:
>> > leopard i686 stable pub v5.1.0
>> >
>> > As an aside I watched your introductory videos and found you to be
>> > very knowledgeable, well-spoken and very helpful in understanding some
>> > of the amazing things you guys are doing for analysis. Really cool to
>> > be emailing you and getting help from the pros.
>> >
>> > Thanks
>> >
>> > Joe
>> >
>> > On Wed, Jul 1, 2015 at 1:12 PM, Bruce Fischl
>> > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > Hi Joe
>> >
>> > what FS version are you using? That certainly looks like a bug,
>> > but maybe
>> > it's one we've fixed already?
>> >
>> > Bruce
>> >
>> >
>> > On Wed, 1 Jul 2015, joseph veliz wrote:
>> >
>> > > Hello Freesrufers,
>> > >
>> > > There are voxels in random areas of the aparc+aseg.mgz that are
>> > categorized
>> > > as 'unknown'.
>> > >
>> > > I read an earlier email stating that aparc+aseg.mgz should not
>> > be directly
>> > > edited by filling in voxels. Correct?
>> > >
>> > > A specific example of this is shown on the attatched images.
>> > >
>> > > aseg.mgz categorizes this area as cortex, yet the aparc+aseg.mgz
>> > does not
>> > > even though it is within pial boundary and is adjacent to other
>> > > (categorized) cortical and sub cortical regions.
>> > >
>> > > How could we go about correcting this?
>> > >
>> > > Thank so much
>> > >
>> > > Joe
>> > >
>> > >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu > 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
>>
>> --
>> 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
>>
>
>
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[Freesurfer] [FreeSurfer] add to color lut for aparc+aseg.mgz

[joseph veliz]

Hello FreeSurfer world,


We need to subdivide regions of the forebrain that FreeSurfer does not.

Is it possible to further subdivide regions of the brain on aparc+aseg.mgz
by defining new colors (& numbers) on the color lut that already defines
structures in Freeview?

Thanks so much


Joseph Veliz
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Re: [Freesurfer] [FreeSurfer] add to color lut for aparc+aseg.mgz

[joseph veliz]

We need to subdivide regions of the VentralDC that would carry onto the
aparc+aseg.mgz.

Would this involve just editing the aseg.mgz?


On Fri, Jul 24, 2015 at 9:27 AM, Douglas Greve 
wrote:

>  For surface ROIs, you'll have to create a new annotation using
> mris_divide_parcellation, the use mri_aparc2aseg to generate a new file
> like aparc+aseg.mgz
> doug
>
>
>
> On 7/23/15 5:09 PM, joseph veliz wrote:
>
>  Hello FreeSurfer world,
>
>
>  We need to subdivide regions of the forebrain that FreeSurfer does not.
>
>  Is it possible to further subdivide regions of the brain on
> aparc+aseg.mgz by defining new colors (& numbers) on the color lut that
> already defines structures in Freeview?
>
>  Thanks so much
>
>
>  Joseph Veliz
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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> 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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[Freesurfer] [FreeSurfer] multicore recons

[joseph veliz]

What is the best set up to utilize the multicore capability of freesurfer?

Should we open a seperate terminal for each subject and run 3 simultaneous
recons with the -openmp 8, on each recon command line?

Or is there a more efficient way of utilizing 8 cores and 16 gb of memory?

thanks so much

joseph
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Re: [Freesurfer] [FreeSurfer] multicore recons

[joseph veliz]

so I should run one subject per 4 cores

by using "-openmp 4" for each of the two subjects being re-conned
simultaneously?

On Fri, Jul 24, 2015 at 2:08 PM, Bruce Fischl 
wrote:

> Hi Joseph
>
> if you have lots to get through you might be better off running two with 4
> cores at a time. Speed increase is pretty good through 4 last time Nick
> tested, but then the benefits fall off a bit
> Bruce
>
>
> On Fri, 24 Jul 2015, joseph veliz wrote:
>
> > What is the best set up to utilize the multicore capability of
> freesurfer?
> >
> > Should we open a seperate terminal for each subject and run 3
> simultaneous recons with the
> > -openmp 8, on each recon command line?
> >
> > Or is there a more efficient way of utilizing 8 cores and 16 gb of
> memory?
> >
> > thanks so much
> >
> > joseph
> >
> >
> >
> >
> ___
> 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] [FreeSurfer] multicore recons

[joseph veliz]

thanks i was not using the -open x , correctly

On Fri, Jul 24, 2015 at 7:37 PM, Z K  wrote:

> Yes. That is correct.
>
> On Jul 24, 2015, at 7:06 PM, joseph veliz  wrote:
>
> so I should run one subject per 4 cores
>
> by using "-openmp 4" for each of the two subjects being re-conned
> simultaneously?
>
> On Fri, Jul 24, 2015 at 2:08 PM, Bruce Fischl 
> wrote:
>
>> Hi Joseph
>>
>> if you have lots to get through you might be better off running two with 4
>> cores at a time. Speed increase is pretty good through 4 last time Nick
>> tested, but then the benefits fall off a bit
>> Bruce
>>
>>
>> On Fri, 24 Jul 2015, joseph veliz wrote:
>>
>> > What is the best set up to utilize the multicore capability of
>> freesurfer?
>> >
>> > Should we open a seperate terminal for each subject and run 3
>> simultaneous recons with the
>> > -openmp 8, on each recon command line?
>> >
>> > Or is there a more efficient way of utilizing 8 cores and 16 gb of
>> memory?
>> >
>> > thanks so much
>> >
>> > joseph
>> >
>> >
>> >
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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Re: [Freesurfer] pial surface from one hemisphere is crossing the surface of other hemishpere

[joseph veliz]

I have also come across this output.

On Fri, Jul 24, 2015 at 6:57 AM, Bruce Fischl 
wrote:

> Hi Antonin
>
> not sure - if you upload the subject I'll take a look
> Bruce
> On Fri, 24 Jul 2015,
> Antonin Skoch wrote:
>
> > Dear experts,
> >
> > I came several times across the situation when pial surface from one
> hemisphere
> > is crossing the surface of other hemishpere (see the attached
> screenshot). Is
> > there any way how to correct for this error?
> >
> > Regards,
> >
> > Antonin Skoch
> >
> >
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[Freesurfer] [FreeSurfer] Version

[joseph veliz]

Is this the 5.3.0 version for snowleopard?

[image: File:]freesurfer-Darwin-snowleopard-i686-dev.tar.gz

4355640 KB 7/31/15 3:31:00 AM





terminal outputs
 freesurfer-Darwin-snowleopard-i686-dev-20150730 

thanks

joe
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