Yes, there are different mgz files for left and right (but they have the same index numbers and colors).
On 10/30/15, 11:16 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
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" greve@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" greve@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.jacobs@maastrichtuniversity.nl >>> wrote: >>> >>>> Thanks! Works wonderful! >>>> Heidi >>>> >>>> On 10/21/15, 10:50 PM, "Douglas N Greve" >>>> greve@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 >>>>> greve@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 > >
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