Dear Petr,

according to the screenshot, the problem is that there is quite low signal intensity in the cut-out parts of gray matter on T2 images.

Apart from HCP pipelines, you can try to increase -nsigma_below parameter of mris_make_surfaces to prevent this cut-out. The default value is 3, try something higher.

Or you can try dev version of freeSurfer and experiment with explicit setting of T2 intensity threshold using -T2_min and -T2_outside_min parameters.

Regards,

Antonin Skoch

You could try with the HCP Pipelines and see if that helps:

https://github.com/Washington-University/PipelinesPeace,

Matt.

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Petr Bednarik bedna...@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 !

PB