Re: [Freesurfer] remove label from aseg
I think this one thread might have disappeared (if not, I apologize for my impatience). Heidi On 10/27/15, 5:16 PM, "Jacobs H (NP)" wrote: >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" 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" >>>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)" > > wrote: > >> Thanks! Works wonderful! >> Heidi >> >> On 10/21/15, 10:50 PM, "Douglas N Greve" >> 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 >>> 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 >>> >>> >>> 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n
Re: [Freesurfer] remove label from aseg
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" 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" 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)" wrote: > Thanks! Works wonderful! > Heidi > > On 10/21/15, 10:50 PM, "Douglas N Greve" > 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 >> 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 >> >> >> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] remove label from aseg
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" 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)" >>> >>> wrote: >>> Thanks! Works wonderful! Heidi On 10/21/15, 10:50 PM, "Douglas N Greve" 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 > 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 > > > 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
Re: [Freesurfer] remove label from aseg
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" 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)" >> >> wrote: >> >>> Thanks! Works wonderful! >>> Heidi >>> >>> On 10/21/15, 10:50 PM, "Douglas N Greve" >>> 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 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 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
Re: [Freesurfer] remove label from aseg
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)" > wrote: > >> Thanks! Works wonderful! >> Heidi >> >> On 10/21/15, 10:50 PM, "Douglas N Greve" >> 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 >>> 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 >>> >>> >>> 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
Re: [Freesurfer] remove label from aseg
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)" wrote: >Thanks! Works wonderful! >Heidi > >On 10/21/15, 10:50 PM, "Douglas N Greve" >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 >>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 >> >> >>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
Re: [Freesurfer] remove label from aseg
Thanks! Works wonderful! Heidi On 10/21/15, 10:50 PM, "Douglas N Greve" 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 >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 > > >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
Re: [Freesurfer] remove label from aseg
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 “old” 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 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 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] remove label from aseg
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 “old” 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 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.