Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes
Hi Johannes,
you can use "label_area", but note that the current version doesn't take into account the reduction in surface area of the average surface relative to all the individuals. We'll need to fix it and get you a new version.
cheers, Bruce On Tue, 31 Oct 2006, Johannes Klein wrote:
Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Johannes,
wm.mgz is produced in the -autorecon2 stage of recon-all.
A handy table to consult is:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
or
http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.h...
Nick
On Tue, 2006-10-31 at 11:49 +0000, Johannes Klein wrote:
Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The problem is that this is being done an the average subject, which does not have a wm.mgz file. Should be easy to fix. Johannes, can you send your cmd line?
doug
Nick Schmansky wrote:
Johannes,
wm.mgz is produced in the -autorecon2 stage of recon-all.
A handy table to consult is:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
or
http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.h...
Nick
On Tue, 2006-10-31 at 11:49 +0000, Johannes Klein wrote:
Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sure, my command would look something like this: mris_anatomical_stats -b average_subject lh white -l lh.mylabel Works on individual subjects, but not on the averaged one. The latter was created with make_average_subject --subjects STRU_1 STRU_2 [...] --out average_subject Thanks for your help, Johannes
Doug Greve schrieb:
The problem is that this is being done an the average subject, which does not have a wm.mgz file. Should be easy to fix. Johannes, can you send your cmd line?
doug
Nick Schmansky wrote:
Johannes,
wm.mgz is produced in the -autorecon2 stage of recon-all.
A handy table to consult is:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
or
http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.h...
Nick
On Tue, 2006-10-31 at 11:49 +0000, Johannes Klein wrote:
Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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Bruce Fischl -
Doug Greve -
Johannes Klein -
Nick Schmansky