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Hello FreeSurfer Developers,
I'm attempting to perform a correction on the reconstruction of lh.white and rh.white surfaces (in excess at baseline), but it doesn't work. I checked the method with another colleague of mine, but both of us are not able to understand why or how to solve this.
The procedure I use is the following (in freeview): 1)Open volume and surface objects with: freeview --volume mri/brainmask.mgz --volume mri/orig.mgz --volume mri/wm.mgz:colormap=heat:opacity=0.4 --surface surf/lh.pial:edgecolor='255,0,0' --surface surf/rh.pial:edgecolor='255,0,0' --surface surf/lh.white:edgecolor='blue' --surface surf/rh.white:edgecolor='blue'.
2) Click on the wm row so that it's highlighted in the top left corner of freeview
3) Select recon edit and then left click + shift to erase parts of the wm volume which I consider to be in excess
4) Save the wm.mgz volume
5) Launch wm and lh or rh.white correction with: recon-all -autorecon2-wm -autorecon3 -subjid $SUBJ
After the conclusion of the correction, I open again freeview and I see that the wm volume corresponds to the one I edited, but the white surfaces are not "updated" to adapt to my correction of wm (see image "before smoothing").
How can I perform a recalculation of the white surfaces from my correction of wm.mgz?
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached a picture of a "not-updated white surface" to make sure I can show you my problem (again, "before smoothing").
On a side note, we tried to circumvent all this by using "Tools - Reposition Surface - Smooth" to slightly smooth the excess white surface (for its effect, see image "after smoothing"). If there is no other way to do it, do you believe this is a good method or are there better ones? Could you please explain me how can I recalculate the stats after smoothing the surfaces?
1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.4 LTS 3) uname -a: Linux vrk-neuro.auxonet.local 5.15.0-119-generic #129-Ubuntu SMP Fri Aug 2 19:25:20 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
Thank you very much for your help.
Kind regards, Alessandro
