For those measures, you can put them onto fsaverage. See mris_preproc
with --meas thickeness or area or volume; that will take all of your
subjects, resample them into fsaverage space, then stack them into one
file (mgz, nii.gz, etc). You can then visualize that file on fsaverage
in freeview, then scroll through all of your subjects with the frame button.
On 4/15/2025 2:09 PM, Stefanie Bradley wrote:
External Email - Use Caution
Ah yes, sorry:
I'm interesting in comparing cortical thickness, total surface area,
and gray matter volume.
And I was wondering about resampling the surfaces to fsaverag,e
because I'd like to be able to visualize the inflated surface of each
subject (in common space?) with overlays as well.
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Tuesday, April 15, 2025 1:51 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] clarification - recon-all output data
But what are you comparing? Eg, thickness, or the white surface (somehow)?
On 4/15/2025 1:26 PM, Stefanie Bradley wrote:
External Email - Use Caution
I'd like to be able to compare different subjects in a common space -
would that require resampling to fsaverage?
Thanks,
Stefanie
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Tuesday, April 15, 2025 1:14 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>; Zollei, Lilla,Ph.D.
<lzol...@mgh.harvard.edu> <mailto:lzol...@mgh.harvard.edu>
*Subject:* Re: [Freesurfer] clarification - recon-all output data
I'm not sure I know what you mean. Why do you want to map them to
fsaverage?
I'm cc'ing Lilla about the age question
On 4/14/2025 11:36 AM, Stefanie Bradley wrote:
External Email - Use Caution
Thank you!
To resample a subject's surfaces to a common space (fsaverage), is
the best way to use mri_surf2surf? E.g., for ?h.inflate, ?h.pial, etc.
And is using fsaverage appropriate to use for pediatric brains (aged
4-6 years old)?
Thanks,
Stefanie
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, April 14, 2025 10:12 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] clarification - recon-all output data
All outputs from recon-all are in native space
On 4/12/2025 5:57 PM, Stefanie Bradley wrote:
External Email - Use Caution
Hi there,
I wanted to clarify about the recon-all output: is it in the
subject's native space or is everything already mapped to fsaverage
space?
For example, is aparc.stats based on the brain in the subject's
native space or has the cortical surface already been transformed
to fsaverage space, and then stats (ex., cortical thickness)
derived after that?
Thanks,
Stefanie
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