Look in recon-all.log to find the command that creates the wmparc.mgz.
Run that command changing the aparc annot to your annot and the output
to a new file name. Look in wmparc.stats; at the top will be an
mri_segstats command line. Copy that command line changing the file
names as needed.
On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
External Email - Use Caution
Thanks!, how can I obtain the white matter volume stats using my
annotation file?
El mar, 16 mar 2021 a las 16:59, Douglas N. Greve
(<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>) escribió:
I think they will give very similar results, but my guess is that
#1 is a little better
On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
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I want to use the annotation file created by myself in fsaverage
to calculate the anatomical stats, but i dont know what is the
best workflow.
1. Convert the annotation file to each subject space using
mri_sur2surf and using mri_anatomical_stats in each subject
2. Convert the surface of each subject to fsaverage space and use
mri_segstats to obtain the data, in this case i dont know what
surface i have to convert to fsaverage space to do it (i can see
thickness (lh/rh.thickness) and volume (lh/rh.volume) but not
folding index and white matter volume)
Any idea?
El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
(<bfis...@mgh.harvard.edu <mailto:bfis...@mgh.harvard.edu>>)
escribió:
Hi Alberto
1. And 4. Are not properties of single surfaces – they are
computed from the white and the pial. For 2 and 3 that is
really up to you
Cheers
Bruce
*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 *Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* [Freesurfer] Problem with freesurfer measures
* External Email - Use Caution *
Hello Freesurfer team, I am using an annotation file that
i've created previously to obtain the measures of some ROIs.
To do that i am using de commands mri_surf2surf and
mri_segstats. I want to obtain the following measures:
1. Gray and White Matter Volume
2. Folding Index
3. Curvature measures
4. Thickness
However I don't know what surface in the surf folder of each
subject I have to use. Could u help me?
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