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 <fis...@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 <fis...@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*
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