Are there different files for the lh and rh? Sorry, never done the subfields analysis.
On 10/30/2015 01:25 PM, Bruce Fischl wrote: > Hi Heidi > > I guess you could do it yourself in matlab using the aseg to figure > out which hemisphere you are in > > cheers > Bruce > > On Fri, 30 Oct 2015, Jacobs H (NP) wrote: > >> >> 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. 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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
