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
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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
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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
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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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-- 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/
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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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-- 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/
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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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-- 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/
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Jacobs H (NP)