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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