Hello freesurfers
I'm trying to reconstruct the pial and white surfaces of the rat. The input image is an inverted T2 (attached) and the segmentation to white and gray matter is done using an in house tool. using the following I'm trying to extract the surfaces: mri_fill -CV 120 128 89 -PV 124 137 111 -PV 123 133 113 -PV 123 136 110 -PV123 134 117 mri/white.mgz mri/filled/filled.mgz mri_pretess mri/filled/filled.mgz 255 mri/brain.mgz mri/filled-pretess255. mgz mri_tessellate mri/filled-pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.smoothwm.nofix surf/lh.inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain ratT1 lh -pial
The white surface(red) is ok, the pial surface(yellow) not at all. Any idea if it's possible to fix it? is it possible to give the gray matter segmentation as an initial guess?
Thanks ! Shani
_______________________________________________ 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.
