Hi, Is there a way to change the index of the segmentation of the hippocampal subfields, so that when I combine left and right, FreeSurfer treats them as different regions?
Thanks! Best Heidi > >>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
