Re: [Freesurfer] remove label from aseg

[Jacobs H (NP)]

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/
>>>
>>> ___
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>>> 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.
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 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] remove label from aseg

[Douglas Greve]

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.
>>>
>
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>
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Re: [Freesurfer] remove label from aseg

[Jacobs H (NP)]

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/

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 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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Re: [Freesurfer] remove label from aseg

[Douglas Greve]

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
>>>
>>>
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Re: [Freesurfer] remove label from aseg

[Jacobs H (NP)]

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.
>>
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
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[Freesurfer] remove label from aseg

[Jacobs H (NP)]

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
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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.

Re: [Freesurfer] remove label from aseg

[Jacobs H (NP)]

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.
>


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Re: [Freesurfer] remove label from aseg

[Douglas N Greve]

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/

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