External Email - Use Caution
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 all the 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 of the
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 of FreeView as 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.FreeView changes: 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
Caution 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_______________________________________________Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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