[Freesurfer] Manual segmentation issues
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.
Re: [Freesurfer] Manual segmentation issues
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 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.
Re: [Freesurfer] Manual segmentation issues
sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3... <https://drive.google.com/file/d/0BzdSon_87KLzYl9SMGJIcGcxakE/view?usp=drive_web> 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 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 >> 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.
Re: [Freesurfer] Manual segmentation issues
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 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 >> 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 t
Re: [Freesurfer] Manual segmentation issues
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 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 > 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 >>> 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.p
[Freesurfer] Remove address
Is it possible to quit the freesurfer mailing list ? Best regards, Antoine ___ 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.
Re: [Freesurfer] Using subject specific template, atlas, & TPM
Hey ! Is it possible not to receive the mails anymore ? Best regards, Antoine Le 11 janv. 2018 18:27, "Ramesh Babu" a écrit : > Dear experts, > > I have analysed T1 data using Freesurfer. Now we have created atlas, > template & tissue probability map using different methods and softwares. I > need your help to use template in freesufer, so that we can compare with > default template and our template. Please help me to put these images in > appropriate folders in Freesurfer. > > > Thank you > RB > > > ___ > 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.
Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
External Email - Use Caution I don't want to be part of this mailing list. Thanks in advance. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
