External Email - Use Caution Hi Bruce,
I tried to upload the whole subject dir in the ftp site but i didn´t works. I send you the file in 7zip format trough a google drive link . I would know how can i extend the pial surface without affect the wm boundaries because the pial surface segmentation in some subjects (as this that i send to you) was incorrect. https://drive.google.com/open?id=11xcWuDlWzGeLLV4MvW-bJK3-rrlsIA8Q Thaks in advance Cheers, 2018-05-01 16:26 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > why don't you tar and gzip the whole subject dir and upload it to our ftp > site and we will take a look > cheers > Bruce > > On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote: > > >> 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 >> >> > _______________________________________________ > 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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