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
Nick:
Congratulations!
Graham
At 3/6/2006 11:59 AM, you 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:
Though we have tested this release thoroughly, we realistically expect that there will be some bugs and kinks to workout. Accordingly, we have added a "Known Issues" section to the release page at:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
We will have a minor release in a week in which these issues will be resolved.
As luck would have it, there are already two issues, one is fairly important, so take note:
* Make sure to run "setenv FIX_VERTEX_AREA" if using any commands outside of recon-all, particularly the mri_glmfit and mri_surfcluster programs. To be safe, you can just add the line "setenv FIX_VERTEX_AREA" into FreeSurferEnv.csh or your .cshrc file. This will only affect those downloading the new version. This will automatically be done for those in the Martinos Center.
* In tkmedit, while loading a functional overlay or time course, the registration file name may not be read properly. A workaround is to load the overlay or time course from the command line (see tkmedit for details).
* My (ie, Doug's) next email will be about a new average subject to replace both the talairach and average7 subjects.
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
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
hi doug this is unrelated to the usage of fsaverage, but i was wondering if the talairach coordinates of this average subject are more compatible with the talairach map than those of average7. thanks, frida On Monday, March 6, 2006, at 06:12 PM, Doug Greve wrote:
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
Yahoo! Groups Links
<*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/
<*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com
<*> Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
Actually, this is still a good question. I took great pains to make sure that the surfaces were in registration with the MNI305, and I'm assuming that this will make the the tal coords match up better. But I never actually sat down and checked various areas against the talairach atlas. Nick might have, though ...
doug
On Tue, 7 Mar 2006, Frida Polli wrote:
hi doug this is unrelated to the usage of fsaverage, but i was wondering if the talairach coordinates of this average subject are more compatible with the talairach map than those of average7. thanks, frida On Monday, March 6, 2006, at 06:12 PM, Doug Greve wrote:
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
Yahoo! Groups Links
<*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/
<*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com
<*> Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
ignore previous email - the README file answers my question - yes. sorry, thnx, f On Monday, March 6, 2006, at 06:12 PM, Doug Greve wrote:
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
Yahoo! Groups Links
<*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/
<*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com
<*> Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
hi doug what i thought you said in this email is that the surface area of average7 is smaller that it should be. however, when i ran label_area with average7 vs. fsaverage, average7 has bigger SAs for the two labels i tried. am i misunderstanding something? again, this is only two labels, and the differences are not huge - about 50 mm2 for ~500 mm2 label - so 10% diff. On Monday, March 6, 2006, at 06:12 PM, Doug Greve wrote:
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
Yahoo! Groups Links
<*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/
<*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com
<*> Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
When you use average7, it turns off "fixing of vertex area", which makes the clusters bigger. The end result, as you've noticed, is that the cluster area is about right :).
doug
Frida Polli wrote:
hi doug what i thought you said in this email is that the surface area of average7 is smaller that it should be. however, when i ran label_area with average7 vs. fsaverage, average7 has bigger SAs for the two labels i tried. am i misunderstanding something? again, this is only two labels, and the differences are not huge - about 50 mm2 for ~500 mm2 label - so 10% diff. On Monday, March 6, 2006, at 06:12 PM, Doug Greve wrote:
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
Yahoo! Groups Links
<*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/
<*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com
<*> Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
but there are label areas not clusters On Friday, March 10, 2006, at 08:39 AM, Doug Greve wrote:
When you use average7, it turns off "fixing of vertex area", which makes the clusters bigger. The end result, as you've noticed, is that the cluster area is about right :).
doug
Frida Polli wrote:
hi doug what i thought you said in this email is that the surface area of average7 is smaller that it should be. however, when i ran label_area with average7 vs. fsaverage, average7 has bigger SAs for the two labels i tried. am i misunderstanding something? again, this is only two labels, and the differences are not huge - about 50 mm2 for ~500 mm2 label - so 10% diff. On Monday, March 6, 2006, at 06:12 PM, Doug Greve wrote:
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
Yahoo! Groups Links
<*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/
<*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com
<*> Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
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
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
Which tool are you using to measure the label area?
Frida Polli wrote:
but there are label areas not clusters On Friday, March 10, 2006, at 08:39 AM, Doug Greve wrote:
When you use average7, it turns off "fixing of vertex area", which makes the clusters bigger. The end result, as you've noticed, is that the cluster area is about right :).
doug
Frida Polli wrote:
hi doug what i thought you said in this email is that the surface area of average7 is smaller that it should be. however, when i ran label_area with average7 vs. fsaverage, average7 has bigger SAs for the two labels i tried. am i misunderstanding something? again, this is only two labels, and the differences are not huge - about 50 mm2 for ~500 mm2 label - so 10% diff. On Monday, March 6, 2006, at 06:12 PM, Doug Greve wrote:
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
Yahoo! Groups Links
<*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/
<*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com
<*> Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
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
Frida Polli PhD Candidate, Suffolk University Research Fellow in Psychiatric Neuroimaging Massachusetts General Hospital CNY 149-2608, 13th Street Charlestown, MA 02129 phone: (617) 724 4604 fax: (617) 726 4078 email: fpolli@nmr.mgh.harvard.edu
I want to bring your attention to a key difference between the "new" reconstruction and the "old" reconstruction. The new recon automatically fills in the ventricles and basal ganglia prior to creating the surface. This creates a different folding pattern, and so the surface registration target has also changed.
The implication is that you should not mix data from "old" and "new" reconstructions in a group analysis. Also, those using the "new" recon should render group results on the new average subject (fsaverage). Those using the "old" recon should continue using average7.
I put "old" and "new" in quotes because a lot of people were using the "new" recon (ie, recon-all-dev) prior to the release.
If you are not sure which atlas you used, then try this:
cd yoursubject/scripts grep GCS recon-all.log
This may produce several lines. Look at the last of the lines for something like:
GCS atlas2002_simple.gcs -----> This means it is the old atlas GCS curvature.buckner40.filled.desikan_killiany.gcs ----> New
Thanks to Frida Polli and Eric Feczko for drawing my attention to this issue.
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
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Frida Polli -
Graham Wideman -
Nick Schmansky