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 greve@nmr.mgh.harvard.edu Reply-To: martinos-tech@yahoogroups.com To: martinos-tech@yahoogroups.com, 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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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