External Email - Use Caution Hi Bruce,
I sent you the whole directory if one subject un which we had some problems extending the pial surface. Se would like extend the pial surface without affect the wm boundary. Did you have a chance to review It? Thanks in advance, Cheers, El vie., 4 may. 2018 1:02, Miguel Ángel Rivas Fernández < miguelrivasf...@gmail.com> escribió: > 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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