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: mharms@wustl.edu

On 9/9/14 7:35 AM, "Bruce Fischl" fischl@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.

Hi Mike

sorry, I never really documented it. Essentially they provide limits on the allowable intensities of the various tissue classes at the different boundaries (gray/white and pial). Unless those constraints are satisfied it will not try to place the boundary in that region

cheers Bruce

On Sat, 13 Sep 2014, Matt Glasser wrote:

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" mharms@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: mharms@wustl.edu

On 9/9/14 7:35 AM, "Bruce Fischl" fischl@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

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