Hi there,
we have various Alzheimer cases, where the FreeSurfer pipeline can occasionally struggle to correctly segment the ventricles, which results in white matter and pial surfaces "leaking" into the ventricles.
I have tried using -bigventricles passed into the autorecon2 stage, but I can't tell if its doing much. I checked the log files, and you can see -bigventricles passed to several binaries such as mri_ca_register and mri_ca_label, so the flag is definitely being passed from the command line.
Is the -bigventricles meant to be used in this way, and what should it be doing?
Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, but I can't find the documentation to say what it does and if I should be using it.
So, we have previously used a technique whereby we run freesurfer once then create a vents image like: mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o vents.mgz --binval 255
and then add this into the wm.mgz to fill some holes in. I have attached two .png files to illustrate the effect. In this example, I have chosen the slice where the surfaces just start to leak into the ventricles. So, on these snapshots, the problem looks quite small, but on other subsequent slices, you can get fairly large leakage into the ventricles.
So, with these options, what would be the best way to cope with very abnormal ventricles?
Many thanks in advance.
Matt Clarkson
Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG
m.clarkson@ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066
