From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Petr Bednarik <bedna028@umn.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, February 20, 2017 at 12:26 PM
To: <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] issues with -T2pial option in v.5.3

Hi everyone,

I am using Freesurfer version 5.3. I tried to refine the pial surfaces by using -T2pial option:

recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial -autorecon3

This step was helpful - e.g. it removed nicely residuals of venous sinuses, but in some subjects it also removed part of the parietal or frontal cortex, while the white matter is appropriately segmented.

https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?dl=0

The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were acquired in the same session (3T Siemens Trio, standard 32 channel coil).

The problem does not seem to be caused by T2 misregistration :

https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0

Question : What could cause this error and how could I extend pial surfaces and get correct final segmentation ?

Thanks a lot !