Have a look at mris_make_surfaces.c, this is how I learned about most of this stuff as the code is pretty well commented (and Bruce telling me things).
Peace, Matt. On 9/12/14, 11:01 PM, "Harms, Michael" <mha...@wustl.edu> wrote: > >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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
