You could try with the HCP Pipelines and see if that helps: https://github.com/Washington-University/Pipelines
Peace, 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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