External Email - Use Caution        


Hi Bruce,


The problem is that the reconstruction of the pial surface is incorrect. I tried to put control points on some voxels but did a wrong reconstruction because in this region there is no voxel with an intensity between 95-110. How can I improve the reconstruction of the pial surface (in this case extend) without modifying the boundaries of wm? . Sorry, I read the answer you gave to Saum but I could not understand very well how to modify the statistics that FreeSurfer does in the mri_make_surfaces.



Hi Saum

it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in 


Thanks,


Cheers,

 

2018-04-29 17:33 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some control points in regions where the intensity is in say [95, 110) and see if that helps

cheers
Bruce


On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote:


        External Email - Use Caution        

Hi guys,


 I have the same problem as Saum, I executed the recon-all in several subjects and I did not obtain a
completely correct segmentation of the pial surface. To solve this error could I use the control
points? When I use the control points, will I also be able to correct the white matter segmentation?

I send you a image if you want
to check it.

Thank you very much!


Cheers,



 [IMAGE]


 

2018-04-27 21:28 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Saum

      it is, but you need to figure out why it isn't getting out far enough. The easiest way
      is to override the intensity statistics that are computed automatically in
      mris_make_surfaces. You can see them if you look in your recon-all.log. For example if
      the lowest value gm is allowed to be at the pial surface is too high, then it will
      settle too far in

      cheers
      Bruce


      On Fri, 27 Apr 2018, Saum Naderi wrote:


                    External Email - Use Caution        

            Hi guys,

            I'm having some trouble extending the pial surface of my bm volume. I am
            aware that the general
            procedure for extending the pial is to extend the wm first and the pial will
            follow. However, is it
            possible to extend the pial surface without affecting the wm boundary?

            Thanks,

            Saum



_______________________________________________
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.




--
Miguel Ángel Rivas Fernández


_______________________________________________
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.




--
Miguel Ángel Rivas Fernández