I think if you delete the ?h.pial files then run
recon-all -s subject -autorecon3 -nosphere -nosurfreg -nowhite -nocortparc
It should regenerate everything with the T1-only pial
On 9/10/2020 12:50 PM, Otília C. d'Almeida wrote:
External Email - Use Caution
Thank you Douglas.
So, as far as I understood, the estimates (cortical thickness for
example) are estimated from rh.pial surface (that comes from FLAIR
pial surface). Since the use of FLAIR decreased the quality of pial
segmentation (GM is underestimated since FLAIR pial surface was drawn
throughout the GM tissue and not along the interface), should I re-run
recon-all without -FLAIRpial flag or is there a way to use T1pial
instead in order to obtain my estimates (I would prefer to check for
small pial errors in this surface) without executing all recon-all
steps? If it is possible, how?
Thanks,
Otília
A 2020-09-10 17:38, Douglas N. Greve escreveu:
rh.pial.T1 is the T1-based surface, rh.pial.FLAIR is the FLAIR-based
surface refined from the T1 surface. rh.pial is the final surface and
is a symbolic link to rh.pial.FLAIR
On 9/10/2020 10:40 AM, Otília C. d'Almeida wrote:
External Email - Use Caution
Hi FS community,
I started using FS 7.1.0 for cortical and subcortical
parcellation/segmentation.
As I found information that FLAIR data could improve pial surfaces
creation, I decided to try it on since I have FLAIR images besides
MPRAGE, by using the command line form FSwiki:
*recon-all -subject NAME -i input_volume.nii -FLAIR FLAIR_volume.nii
-FLAIRpial -all*
However when I opened Freeview, I overlaid *rh.pial*, and
*rh.pial.FLAIR, rh.pial.T1*.
The first two are quite similar (overlap) and the segmentation is
worse than rh.pial.T1.
So, my question is, what is really the final surface of recon-all
that must be checked for errors and that is used for stats estimation?
Thank you in advance.
Best regards,
Otília
_______________________________________________
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 <mailto: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
