I think this one thread might have disappeared (if not, I apologize for my impatience). Heidi
On 10/27/15, 5:16 PM, "Jacobs H (NP)" <h.jac...@maastrichtuniversity.nl> wrote: >I just checked again in freeview and indeed they have the same index (e.g. >CA1 has value 206 for left and also for right). > >On 10/27/15, 5:01 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >>The color is not important. The question is whether they have a >>different index. Can you confirm that lh and rh have the same index? >> >>On 10/27/15 11:53 AM, Jacobs H (NP) wrote: >>> Hi Doug, >>> >>> Yes, for the aseg they are. But not for the hippocampal subfields: left >>> and right have the same color coding. >>> I am creating one segmentation, including left and right hippocampal >>> subfields and aparc, for partial volume correction. >>> Any idea how I can make the labels for the hippocampal subfields >>>different >>> (freesurfer version 6)? >>> >>> Thanks >>> Heidi >>> >>> On 10/27/15, 4:32 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >>>wrote: >>> >>>> The indices should be different. Eg, 17 is left hippo, 53 is right >>>> hippo. If you click on them in freeview and different labels appear, >>>> then FS knows they are different >>>> >>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote: >>>>> Hi. >>>>> >>>>> Just one another related question: now that I was able to combine >>>>>left >>>>> and >>>>> right hippocampal subfields with the aparc-aseg correctly, I noticed >>>>> that >>>>> the left and right hippocampal subfields have the same color labels >>>>>and >>>>> codes. What would be the best way to make sure that FreeSurfer >>>>> understand >>>>> that the left and right subfields (e.g. Left and right CA1) are >>>>> different >>>>> areas? >>>>> >>>>> Thanks! >>>>> Heidi >>>>> >>>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)" >>>>> <h.jac...@maastrichtuniversity.nl> >>>>> wrote: >>>>> >>>>>> Thanks! Works wonderful! >>>>>> Heidi >>>>>> >>>>>> On 10/21/15, 10:50 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>> wrote: >>>>>> >>>>>>> If you want to remove them, you can use mri_binarize with the >>>>>>> --replace >>>>>>> option, replacing them with whatever you want. >>>>>>> >>>>>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote: >>>>>>>> Hi, >>>>>>>> >>>>>>>> I am trying to generate a segmentation file containing the >>>>>>>>aseg+aparc >>>>>>>> but replacing the hippocampus with the hippocampal subfields. >>>>>>>> With mergeseg I was able to merge the segmentations, but >>>>>>>> unfortunately >>>>>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in >>>>>>>> there (as the area covered by the subfields is not 100% equal to >>>>>>>>the >>>>>>>> hippocampus of the aseg). >>>>>>>> How can I remove the remains of the old hippocampal labels? >>>>>>>> >>>>>>>> Many thanks! >>>>>>>> Best >>>>>>>> Heidi >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> gr...@nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> Outgoing: >>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer@nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
