Hi Bruce, I was wondering if there is info somewhere about what each of those 7 MIN_ and MAX_ variables control regarding the positioning of the white and pial surfaces?
thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu On 9/9/14 7:35 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Andrea > >what is the background image? This is usually either a failure of the >intensity normalization or of the surface deformation/segmentation to >adaptively estimate the underlying intensity distributions of the >gray/white matter. If you look in recon-all.log for that subject you will >find a set of lines like: > >setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) >setting MAX_BORDER_WHITE to 112.0 (was 105) >setting MIN_BORDER_WHITE to 83.0 (was 85) >setting MAX_CSF to 59.1 (was 40) >setting MAX_GRAY to 100.0 (was 95) >setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75) >setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40) > > > >in your case for example you will probably find that the min_border_white >is too high or tha the max_gray is too low. You can set these using the >expert opts for both mri_segment and mris_make_surfaces. > >cheers >Bruce > > >On Tue, 9 Sep 2014, Andrea >Horváth wrote: > >> Dear Freesurfers, >> >> >> After running recon-all, the wm surfaces are too close to the pial >>surface, >> some gray matter is segmented as white matter as seen in the attached >> picture (red cross: a bigger cortical part is included in the white >>matter). >> >> How can I shrink the wm surface? >> >> Thank you for your help! >> >> Andrea >> >> >> >> >> >> >> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ 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.
