Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

[Douglas N. Greve]

Yes, that is correct

On 12/20/2023 2:07 PM, Edwards, Vincent wrote:


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Hi,

I'm following up on my quick question from this time last week.

I have several brains that I sent through recon-all using Freesurfer 
7. If I wanted to use Freeview on Freesurfer version 5 to do 
pial/wm/and control point edits, would I be able to do recon-all 
through Freesurfer 7?  Years ago, someone asked if they could do 
recon-all in an older version of Freesurfer and edit in a newer GUI. 
Doug said that was fine. My question is basically the inverse of their 
problem. I assumed that since Freeview is a GUI, the version used 
shouldn't have any actual impact on things as long as we returned to 
version 7 to recon-all. I just want to confirm that my assumption is 
correct?


The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 
(recon-all for pial/wm/cp's)


Thanks,
Vincent Edwards

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Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

[Douglas N. Greve]

Yes, that is correct.

On 12/13/2023 3:01 AM, Edwards, Vincent wrote:


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Hello,

I have several brains that I sent through recon-all using Freesurfer 
7. If I wanted to use Freeview on Freesurfer version 5 to do 
pial/wm/and control point edits, would I be able to do recon-all 
through Freesurfer 7? I assumed that since Freeview is a GUI, the 
version used shouldn't have any actual impact on things as long as we 
returned to version 7 to recon-all. That seemed to be the case when 
someone asked a similar question (the reverse) 
 , 
but that was many years ago so I wanted to confirm.


Thanks,

Vincent Edwards

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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 Mass General Brigham 
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Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

[fsbuild]

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The freesurfer 6.X and 7.x release release notes summarize some changes for 
Freeview (listed below) since version 5 was released in 2013.  If none of 
the improvements in features/stability are relevant to what you are doing, then 
I don’t see why you could not revert to the older 5.X software. But if 
you run into issues with a now ~10 year old version of Freeview, we may tell 
you to use the latest 7.4.1 release from June of 2023.
- R.
- - - - -

•New: interface for x virtual frame buffer (fsxvfb). When you run 
freeview from fsxvfb, no X server is needed. This is good for taking a bunch of 
pictures when you don't want freeview popping up allthe time. Eg, fsxvfb 
freeview orig.mgz -ss mypic.png —quit
•The filled.mgz can now be edited instead of the wm.mgz. The 
advantage to this is that filled.mgz is slightly further in the process and it 
is more intuitive. The filled.mgz is actually a segmentation ofthe 
subcortical mass. In Freeview, you can view it in outline mode, meaning that 
the edges of the segmentations are actually the surface that you are editing. 
After that, run recon-all with the -autorecon2-wm -autorecon3 options, just as 
you would if you had edited the wm.mgz..Landmark-based repositioning of 
surfaces. Did you ever want to just make the surface move through a certain 
point? You can do that now by creating point sets in freeview. Create a 
separate point set for each surface (lh, rh, white, and pial), then save it in 
subject/surf with a file name repos.$hemi.$surf.json where $hemi is either lh 
or rh and $surf is either white or pial. Then run recon-all with the 
-autorecon2-surfonly -autorecon3 options. Note that you can do this 
interactively inside ofFreeViewas well; look under 
Tools-Resposition Surface. If you do it interactively, the surface may be 
overwritten next time recon-all is re-run, but it gives you a chance to play 
with the repositioning.freeview - can now load and visualize diffusion 
orientation distribution function (ODF) data.FreeViewchanges: surfce path 
and label editing, surface annotation editing, automatic segmentation assisted 
by Geodesic Matting algorithm, displaying two time courses at the same time, 
better support for Mac (petsc error fixed on Mac)

On Dec 20, 2023, at 14:07, Edwards, Vincent 
vincent.edwa...@utdallas.edu 
wrote:External Email - Use 
CautionHi,I'm following 
up on my quick question from this time last week.I have several brains 
that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview 
on Freesurfer version 5 to do pial/wm/and control point edits, would I be able 
to do recon-all through Freesurfer 7? Years ago, someone asked if they 
could do recon-all in an older version of Freesurfer and edit in a newer GUI. 
Doug said that was fine. My question is basically the inverse of their 
problem.I assumed that since Freeview is a GUI, the version used 
shouldn't have any actual impact on things as long as we returned to version 7 
to recon-all.I just want to confirm that my assumption is correct?The 
pipeline would be: F7 (recon-all), F5 (edit with freeview),F7 (recon-all 
for pial/wm/cp's)Thanks,Vincent 
Edwards___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Freesurfer/Freeview Version Compatibility

[Edwards, Vincent]

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Hi,

I'm following up on my quick question from this time last week.

I have several brains that I sent through recon-all using Freesurfer 7. If I 
wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point 
edits, would I be able to do recon-all through Freesurfer 7?  Years ago, 
someone asked if they could do recon-all in an older version of Freesurfer and 
edit in a newer GUI. Doug said that was fine. My question is basically the 
inverse of their problem. I assumed that since Freeview is a GUI, the version 
used shouldn't have any actual impact on things as long as we returned to 
version 7 to recon-all. I just want to confirm that my assumption is correct?

The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all 
for pial/wm/cp's)

Thanks,
Vincent Edwards
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[Freesurfer] Freesurfer/Freeview Version Compatibility

[Edwards, Vincent]

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Hello,

I have several brains that I sent through recon-all using Freesurfer 7. If I 
wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point 
edits, would I be able to do recon-all through Freesurfer 7? I assumed that 
since Freeview is a GUI, the version used shouldn't have any actual impact on 
things as long as we returned to version 7 to recon-all. That seemed to be the 
case when someone asked a similar question (the reverse) 

  , but that was many years ago so I wanted to confirm.

Thanks,

Vincent Edwards
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