Works perfectly! Thank you so much! Heidi
On 11/3/15, 6:54 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
In that case you can do something like fscalc lhfile.mgz add 1000 -o lhfile1000.mgz mri_mask lhfile1000.mgz lhfile.mgz lhfile1000.mgz
This will add 1000 to the lhlabels. This will make the lh labels different from the rh. You can add a constant to the rh too if you want.
doug
On 10/30/2015 07:12 PM, Jacobs H (NP) wrote:
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 >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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/
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