Re: [Freesurfer] Scanner and Freesurfer-version differences

[Douglas N. Greve]

On 7/1/2024 1:05 AM, Bronwyn Overs wrote:


External Email - Use Caution

Hi Freesurfer Mailing List,

I work on a large bipolar disorder imaging study that has been running 
for over 10 years. We previously acquired 2 sMRI time-points (pre 
2013, /n/~500, /n/~250 at each time-point) on a single Philips 3T 
scanner and these images were processed with Freesurfer version 5.3. 
We have just now acquired a third imaging time-point that was 
completed on a different scanner (Siemans, /n/~120) using a different 
acquisition protocal. So I have three questions for the mailing list, 
that I'm hoping will inform the design of our analysis protocol:


 1. Are there specific considerations for processing structural MRIs
that have been acquired on different scanners and with different
acquisition protocols?

No, we don't have anything special for this. Our experience is that the 
cortical results tend to be much less dependent upon the actual 
acquisition parameters and scanners.


 1. Reprocessing all time 1 and time 2 images with a newer version of
Freesurfer is a huge undertaking (for both processing time and
personnel time required to review and edit). However, is there a
reason why a newer version of Freesurfer should be used (e.g.
publication considerations, more consistent output) as opposed to
processing time 3 with v5.3?

I think you are ok to continue to use 5.3. Reviewers are pretty lenient 
about these kind of thing. Given the incremental longitudinal nature of 
the project, you can just switch and rerun everything.


 1. I know there are differences in the output across different
versions of Freesurfer. However, do different system set ups (e.g.
linux, mac, as well as operating systems) have an impact on the
output, even if the same version of Freesurfer is used?

You can get differences that are very small but systematic. If it is 
something you are worried about, treat the OS as another variable in the 
sense that you randomize the OS across your variables of interest (ie, 
don't have all your patients be from one OS and all your controls be 
from another). You could test the effect of OS; if it is not 
significant, you can remove it from the analysis.


Kind regards,


Bronwyn Overs

Research Assistant


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1725


neura.edu.au 

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Re: [Freesurfer] freesurfer as module

[fsbuild]

External Email - Use Caution

 My understanding is that it is up to the sysadmins who run a cluster to 
choose how to present and configure the apps they host whether it be thru 
modules, spack, or other tools.  We don't track how cluster admins do 
that, but you could ask the helpdesk for the cluster you are going to use 
(which presumably lists there is some version of freesurfer already available 
on the cluster).  Most have online documentation stating how to run their 
apps.
I have used Freesurfer in the past on the SDSC cluster, and according to their 
web pages, they do use 
modules,https://www.sdsc.edu/support/user_guides/expanse.html#software

- R.

On 7/1/24 14:55, Dong, Yilei (yid...@health.ucsd.edu) wrote



  

  
Hi Freesurfer Developers, 

  


  

  
If Freesurfer is available as a module on a computer cluster, is it 
still necessary to source/configure the freesurfer module in a .bashrc 
script on Linux? 

  


  

  
Sincerely,

  
Yilei 




  

  
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Re: [Freesurfer] Calculating intensity of Individual voxel

[ERNEST KISSI]

External Email - Use Caution

When I tried this , I got 0.0. I have attached a screenshot of it.


[image: image.png]


On Fri, Jun 21, 2024 at 2:47 PM Huang, Yujing 
wrote:

> ‘mri_info vol.mgz --voxel c r s’ will print the voxel value from col row
> slice of all frames.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI
> *Sent:* Friday, June 21, 2024 5:16 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Calculating intensity of Individual voxel
>
>
>
> *External Email - Use Caution*
>
> Hi, freesurfer team
>
>
>
> Is there a way to calculate the intensity of a voxel.Let say, I have a
> voxel with coordinate 20, 30 and 34 and I wanna know the intensity of it.
> Can it be done in 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 Mass General
> Brigham Compliance HelpLine at
> https://www.massgeneralbrigham.org/complianceline <
> https://www.massgeneralbrigham.org/complianceline> .
>
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Re: [Freesurfer] Calculating intensity of Individual voxel

[Huang, Yujing]

Replace [c r s] with voxel coordinates that you are interested in.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Tuesday, July 2, 2024 2:52 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Calculating intensity of Individual voxel


External Email - Use Caution
When I tried this , I got 0.0. I have attached a screenshot of it.


[cid:image001.png@01DACC90.A62265C0]

On Fri, Jun 21, 2024 at 2:47 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
‘mri_info vol.mgz --voxel c r s’ will print the voxel value from col row slice 
of all frames.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of ERNEST KISSI
Sent: Friday, June 21, 2024 5:16 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Calculating intensity of Individual voxel


External Email - Use Caution
Hi, freesurfer team

Is there a way to calculate the intensity of a voxel.Let say, I have a voxel 
with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be 
done in freesurfer?
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Re: [Freesurfer] Freeview cannot be opened (MacOS)

[fsbuild]

External Email - Use Caution

 

If you prefer to run the last stable release (7.4.1),
 then I suggest downloading and installing the Intel binary package 
installer, 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.pkg ;
  To bypass some security prompts, right click on the package file and 
then choose "open will default ..."

You should check the path, but I think you would set things up in the (bash) 
shell as,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1... source the 
environment setup script ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

  

If you don't mind running the latest development build (which can be 
unstable), then you can try the native arm64 binary package installer 
via the link, 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev-20240327.pkg  ;
 Install the same way via right click as listed above.  Then check the 
path, e.g,
$ export FREESURFER_HOME=/Applications/freesurfer/dev... source the environment 
setup script  ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

  

Assuming you have your license file setup, e.g., to be read via 
FS_LICENSE environment variable with license.txt under your home 
directory,

$ export FS_LICENSE=$HOME/license.txt

  

- then it should work to run freeview.  I would first try running 
freeview from the shell command line w/o any arguments to see if it opens an 
empty window.  

$ freeview

  

Then exit and try it again with a known to be good volume, 

$ freevivew $SUBJECTS_DIR/bert/mri/brain.mgz

  

- R.



On 7/1/24 13:42, Melih Keskin (keskinmeli...@gmail.com) wrote:



  External Email - Use 
Caution
  Hi,
I am trying to open Freeview 
using my M1 Macbook (Monterey version 12.5). I am posting the error it 
gives me below. I followed the steps from the below thread but none of 
the solutions worked (mainly changing the privacy settings and getting a
 new Freesurfer 
license). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70979.html

Is there a solution to this problem as of 2024?
Thank you in advance,Melih






2024-07-01
 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method 
userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It
 should not be used in new applications. Use convertRectToBacking: 
instead. 
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[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 Melihs-MacBook-Pro.local by 
keskin Mon Jul  1 20:41:01 2024
[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

  

  
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Re: [Freesurfer] freesurfer as module

[Dong, Yilei]

External Email - Use Caution

Thank you very much!



From: fsbuild 
Sent: Tuesday, July 2, 2024 11:23 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freesurfer as module


My understanding is that it is up to the sysadmins who run a cluster to choose 
how to present and configure the apps they host whether it be thru modules, 
spack, or other tools.  We don't track how cluster admins do that, but you 
could ask the helpdesk for the cluster you are going to use (which presumably 
lists there is some version of freesurfer already available on the cluster).  
Most have online documentation stating how to run their apps.

I have used Freesurfer in the past on the SDSC cluster, and according to their 
web pages, they do use modules,
https://www.sdsc.edu/support/user_guides/expanse.html#software

- R.

On 7/1/24 14:55, Dong, Yilei (yid...@health.ucsd.edu) wrote
Hi Freesurfer Developers,

If Freesurfer is available as a module on a computer cluster, is it still 
necessary to source/configure the freesurfer module in a .bashrc script on 
Linux?

Sincerely,
Yilei



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 .
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Re: [Freesurfer] Scanner and Freesurfer-version differences

[Bronwyn Overs]

External Email - Use Caution

Hi Douglas, 

Thank you so much for your replies. This is extremely helpful. 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



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From: "Douglas N. Greve"  
To: "Freesurfer support list"  
Sent: Tuesday, July 2, 2024 11:31:16 PM 
Subject: Re: [Freesurfer] Scanner and Freesurfer-version differences 



On 7/1/2024 1:05 AM, Bronwyn Overs wrote: 




External Email - Use Caution 
Hi Freesurfer Mailing List, 

I work on a large bipolar disorder imaging study that has been running for over 
10 years. We previously acquired 2 sMRI time-points (pre 2013, n ~500, n ~250 
at each time-point) on a single Philips 3T scanner and these images were 
processed with Freesurfer version 5.3. We have just now acquired a third 
imaging time-point that was completed on a different scanner (Siemans, n ~120) 
using a different acquisition protocal. So I have three questions for the 
mailing list, that I'm hoping will inform the design of our analysis protocol: 


1. Are there specific considerations for processing structural MRIs that 
have been acquired on different scanners and with different acquisition 
protocols? 


No, we don't have anything special for this. Our experience is that the 
cortical results tend to be much less dependent upon the actual acquisition 
parameters and scanners. 

BQ_BEGIN



1. Reprocessing all time 1 and time 2 images with a newer version of 
Freesurfer is a huge undertaking (for both processing time and personnel time 
required to review and edit). However, is there a reason why a newer version of 
Freesurfer should be used (e.g. publication considerations, more consistent 
output) as opposed to processing time 3 with v5.3? 

BQ_END
I think you are ok to continue to use 5.3. Reviewers are pretty lenient about 
these kind of thing. Given the incremental longitudinal nature of the project, 
you can just switch and rerun everything. 

BQ_BEGIN



1. I know there are differences in the output across different versions of 
Freesurfer. However, do different system set ups (e.g. linux, mac, as well as 
operating systems) have an impact on the output, even if the same version of 
Freesurfer is used? 

BQ_END
You can get differences that are very small but systematic. If it is something 
you are worried about, treat the OS as another variable in the sense that you 
randomize the OS across your variables of interest (ie, don't have all your 
patients be from one OS and all your controls be from another). You could test 
the effect of OS; if it is not significant, you can remove it from the 
analysis. 

BQ_BEGIN




Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



[ https://twitter.com/neuraustralia | Twitter ] | [ 
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ 
http://www.neura.edu.au/help-research/subscribe | Subscribe ] 



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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ] 

BQ_END


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