PS: For instance you can notice that the added voxels in the axial slice, coordinates * -39.69, 10.78, 11.54*were not included in the surface. By the way, the subject is 13 months old.
On Tue, May 10, 2016 at 5:06 PM, Saturne Fox <saturne....@gmail.com> wrote: > Bruce, > > I just uploaded the directory through the FTP server, the name of the > archive is 00M034.tar.gz . > > Concerning our issue we tried to identify the problem in the light > of your advices and we observed that > the *orig *file contains most of the manual modifications, which are then > lost in *?h.white*. We spotted some topological > errors but since the *orig *file is created after the topological > corrections and that this file mainly suits us, we don't think > that it is the main source of error. > > Thus, we would like to know what is the influence of the variables > used during the creation of the* ?h.white* surface and how > we can increase the consideration brought to the added voxels. More > precisely, when using the* aseg.presurf* file must the added > voxels be part of the segmented white matter to be taken into account in > the *?h.white* surface ? > As well, we would like to know if 250 is an appropriate intensity to > manually add voxels. > > Best regards, > Antoine > > On Mon, May 9, 2016 at 6:06 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> Hi Antoine >> >> we need the entire subject directory tarred and gzipped if you want us to >> look. And please upload it to our ftp site >> >> thanks >> Bruce >> >> >> On Mon, 9 May 2016, Saturne Fox wrote: >> >> [icon_10_generic_list.png] >>> sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3...[x_8px.png] >>> >>> Dear Bruce, >>> >>> Most of the time the added voxels are included in the orig file >>> but are lost in the ?h.white one. >>> >>> Here is the subject file. >>> >>> Thanks a lot for your help >>> >>> Antoine >>> >>> >>> >>> On Mon, May 9, 2016 at 3:42 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Antoine >>> >>> if you upload the entire subject dir we will take a look. It >>> sounds like it might be a topological defect. You can >>> check this by seeing if the orig.nofix contains the voxels that >>> you added, but the orig does not. >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 9 May 2016, Saturne Fox wrote: >>> >>> Dear freesurfer users, >>> >>> I need your help concerning manual segmentation >>> issues. >>> >>> In fact I used the editing tool with an intensity of >>> 250 to add some >>> missing part on the wm.mgz file but some of the added areas >>> were not >>> considered for the creation of the surface. >>> >>> Some of the added parts were only connected through >>> one voxel to >>> the existing parts and I guess that it might have prevented >>> the surface to >>> include these areas but in some other cases the >>> supplementary parts were >>> clear and connected by two or more voxels but were not added. >>> >>> Do you know what are the criteria used by >>> recon-all to determine the surface ? >>> Do you have advices about how to add voxels and be >>> sure that they will be >>> included in the surface? >>> >>> Best regards, >>> Antoine >>> >>> >>> On Mon, May 9, 2016 at 3:25 PM, Saturne Fox < >>> saturne....@gmail.com> wrote: >>> Dear freesurfer users community, >>> >>> I need your help concerning manual segmentation >>> issues. >>> >>> >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >>> >> _______________________________________________ >> 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. >> >> >
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