I am re-sending an email that Doug wrote earlier this week, as it was a
thorough description of some pretty important changes to the average
subject and talairach subject.
There is a new average subject to replace average7 that ALSO replaces the
talairach subject. It is called "fsaverage" and can be found in the
distribution itself (no additional downloads needed):
$FREESURFER_HOME/subjects/fsaverage
as an additional note, fsaverage can only be used with subjects processed
the new way (i.e., with automatic filling of the entire ventricle).
Another average subject that will be compatible with subjects processed
the old way (i.e., manual editting of the wm) will be available soon.
Please read Dougs email below if you missed it!!
Jenni
---------- Forwarded message ----------
Date: Mon, 06 Mar 2006 18:12:55 -0500
From: Doug Greve <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED]
To: [EMAIL PROTECTED],
Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Subject: [martinos-tech] New average subject and stable release, v3.0
Sorry in advance for the long email ...
We have a new average subject that we are recommending that people use
instead of "average7". This subject can also replace the "talairach"
subject as well. The name of the "fsaverage", and it can be found in
the distribution itself:
$FREESURFER_HOME/subjects/fsaverage
To set up a link in your SUBJECTS_DIR, do the following:
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage
There is a README file in $FREESURFER_HOME/subjects/fsaverage that
describes how this subject was created.
IMPORTANT:
Differences between average7 and fsaverage, and FIX_VERTEX_AREA with
impacts on mri_surfcluster and mri_glmfit.
As some people have noted, the total surface area of average7 was much
less than that of a typical subject (by about 40%). This caused the
areas of clusters as reported by mri_surfcluster to be too
small. HOWEVER, a bug in the routine that computed the vertex area
caused the clusters to be 50% too large. So, the net effect was that
the clusters were about the right size :).
Stay with me.
The surface area of the new average subject (fsaverage) is that of a
typical subject, SO, it is IMPORTANT that it be used in conjunction
with the fixed vertex area.
This affects only two programs: mri_surfcluster and mri_glmfit. After
today (March 6, 2006), if you use average7 with mri_surfcluster or
mri_glmfit, they will give the following error:
ERROR: you have selected subject average7. It is recommended that
you use the fsaverage subject in $FREESURFER_HOME/subjects.
If you really want to use average7, re-run this program with
--really-use-average7 as the first argument.
If you chose to do so, then it will print out:
INFO: you have selected subject average7 (and REALLY want to use it)
instead of fsaverage. So I'm going to turn off fixing of vertex area
to maintain compatibility with the pre-stable3 release.
The results should be the same as when you ran it prior to the stable3
release.
If you have used average7 along with Monte Carlo or Permutation
simulation, inferences based on those simulations should still be
correct. The only problem will be that the cluster area might be a
little different.
If you have used a non-average subject as your common surface space or
an average subject that you created prior to March 1, 2006, then the
cluster sizes will appear to drop by a third the next time your run
mri_glmfit or mri_surfcluster. Again, any mri_glmfit simulation
results will still be valid. For backwards compatibility, you can
add --no-fix-vertex area to either mri_surfcluster or mri_glmfit.
The new versions of mri_surfcluster or mri_glmfit will include the
following line in their summary/logfile output:
# FixVertexAreaFlag 1
The value will either be 1 or 0 depending upon whether it was fixed or
not fixed.
Again, sorry for the long-winded email. I know this is pretty
confusing, so don't hesitate to write with questions as we get this
sorted out. PLEASE send questions to the group to help in this
process.
thanks
doug
Nick Schmansky wrote:
Freesurfer community,
A new stable release, v3.0, is now available.
The Release Notes page describing what's new,
and a link to the download page, is here:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
All users, including those using prior 'dev'
releases, are encouraged to upgrade to this
release.
Updates to the stable release will be issued
if major bugs are found (and fixed), and as
new features which do not affect existing
functionality become available.
The Freesurfer development team
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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