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The labels are derived from ASHS- but yes they are registered to each subject
seperately. Could I ask then what the tutorial refers to- for future reference?
When is it best to go through fsaverage?
Thank you for the information
BW,
Marianna
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Από: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> εκ μέρους του Douglas N. Greve
<dgr...@mgh.harvard.edu>
Στάλθηκε: Δευτέρα, 10 Μαΐου 2021 4:30 μμ
Προς: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Θέμα: Re: [Freesurfer] volume ROI to surface for cortical thickness
did you draw the labels on each subject separately? In that case there is no
need to go through fsaverage.
Projfrac is the fractional distance between the white and pial surfaces (0.5 is
half way)
projdist is the absolute distance (eg, 1.5 is 1.5mm)
Generally projfrac is preferred as it adapts to changes in thickness
In your case, you might want to use --projfrac-max where it will look over a
range of projfrac values for the maximum. This might make your maps look better
because it will be sampling the label or nothing.
On 5/10/2021 12:25 PM, M Pope wrote:
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Dear Freesurfer experts,
I have created volumetric ROIs of entorhinal cortex regions and have registered
them to subjects’ native space (T1). I now wish to register them to the subject
surface in order to get information such as cortical thickness- using
mri_vol2surf and mri_segstats I believe.
I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free
Surfer Wiki
(harvard.edu)<https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4tQELHhKC8hdSICHCc37zU4RhxeFcSeVly9rOphRN2XP-Hn6K3WQXbHVlzOaVeiAALFEEDsWW4Hlf1gOUgdlDeO1QVq5KumypG9Qk5hAOdZ6Othr5MGzujz9YqESMrcJREtyb3JHfB9Lq8ESK7pnmQ52E9DXwDsqbRCXXtKxYi4H1bAPwJUSTSteDzgYRyGUaGAnZcISKs0tuAXnMqHAu2AalzfMJvAfOp4Rk5KvjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness>
and had a few questions.
First of all- could you explain why you are going through fsaverage. Is there
some kind of advantage to doing this procedure of registration, mri_vol2surf
and then mri_surf2surf rather than just using mri_vol2surf with the subject
space as the regheader?? When I tried through fsaverage as explained in the
tutorial (following the exact same commands) the ROI appeared wrong in the
surface and the thickness stats were incorrect.
Secondly, when doing the procedure as per the tutorial, do you mean that we
have to register each subject's mask to the fsaverage- or only one, e.g a ROI
derived from the subject-specific group template (we have one produced through
ANTs).
Lastly- some explanation about how projfrac and projdist work would be very
helpful. What numbers are considered best practice?
Thankyou,
Marianna Pope
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