Re: [Freesurfer] cortical surface area calculation

[Douglas N. Greve]

Yes, it will

On 8/7/2020 6:27 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Hi all,

Does this command  calculate the Cortical Surface Area without the 
non-cortical Medial Wall??


mris_calc --label ../label/lh.cortex.label lh.area stats

Jim



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return 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] cortical surface area

[Alexopoulos, Dimitrios]

Thank you for the input.

Jim

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Friday, October 13, 2017 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical surface area

The 2nd is the one you want as the first one includes non cortical structures 
in the medial wall.


On 10/12/17 6:35 PM, Alexopoulos, Dimitrios wrote:
> Thanks.
>
> I ran this command:
> mris_anatomical_stats subjectID lh pial
> It gave me a total surface area of 115007 mm^2
>
> I also tried the following command from within the 'label' directory:
> mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh 
> pial
> It gave me a total surface area 109458 mm^2
>
> Which is the correct method and value for total cortical surface area?
>
> Jim
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, October 12, 2017 5:17 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] cortical surface area
>
> oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject
> via:
>
> mris_anatomical_stats   pial
>
> cheers
> Bruce
> On Thu, 12 Oct 2017,
> Alexopoulos, Dimitrios wrote:
>
>> I don't see this file in the stats directory using FS 5.3.
>>
>> Jim
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
>> Fischl
>> Sent: Thursday, October 12, 2017 4:52 PM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] cortical surface area
>>
>> Hi Jim
>>
>> check the ?h.aparc.pial.stats file. I think the total surface area should be 
>> in there.
>>
>> cheers
>> Bruce
>> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote:
>>
>>> Specifically, where in the aparc.stats file (or other file) is the cortical 
>>> surface area?
>>> I only see default output for  'WhiteSurfArea'.
>>>
>>> Jim
>>>
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>> N Greve
>>> Sent: Thursday, October 12, 2017 4:16 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] cortical surface area
>>>
>>> mm2
>>>
>>>
>>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>>>> What measure is for the cortical surface area?
>>>>
>>>> The measure in the aparc.stats file states 'WhiteSurfArea'
>>>>
>>>> Jim
>>>>
>>>> 
>>>> -
>>>> -
>>>> --
>>>>
>>>> The materials in this message are private and may contain Protected
>>>> Healthcare Information or other information of a sensitive nature.
>>>> If you are not the intended recipient, be advised that any
>>>> unauthorized use, disclosure, copying or the taking of any action in
>>>> reliance on the contents of this information is strictly prohibited.
>>>> If you have received this email in error, please immediately notify
>>>> the sender via telephone or return mail.
>>>>
>>>>
>>>>
>>>> ___
>>>> 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

Re: [Freesurfer] cortical surface area

[Douglas Greve]

that is the area of the white matter surface in mm2


On 10/12/17 2:15 PM, Alexopoulos, Dimitrios wrote:


What measure is for the cortical surface area?

The measure in the aparc.stats file states ‘WhiteSurfArea’

Jim



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return 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


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] cortical surface area

[Douglas Greve]

The 2nd is the one you want as the first one includes non cortical 
structures in the medial wall.


On 10/12/17 6:35 PM, Alexopoulos, Dimitrios wrote:
> Thanks.
>
> I ran this command:
> mris_anatomical_stats subjectID lh pial
> It gave me a total surface area of 115007 mm^2
>
> I also tried the following command from within the 'label' directory:
> mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh 
> pial
> It gave me a total surface area 109458 mm^2
>
> Which is the correct method and value for total cortical surface area?
>
> Jim
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, October 12, 2017 5:17 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] cortical surface area
>
> oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject
> via:
>
> mris_anatomical_stats   pial
>
> cheers
> Bruce
> On Thu, 12 Oct 2017,
> Alexopoulos, Dimitrios wrote:
>
>> I don't see this file in the stats directory using FS 5.3.
>>
>> Jim
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
>> Fischl
>> Sent: Thursday, October 12, 2017 4:52 PM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] cortical surface area
>>
>> Hi Jim
>>
>> check the ?h.aparc.pial.stats file. I think the total surface area should be 
>> in there.
>>
>> cheers
>> Bruce
>> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote:
>>
>>> Specifically, where in the aparc.stats file (or other file) is the cortical 
>>> surface area?
>>> I only see default output for  'WhiteSurfArea'.
>>>
>>> Jim
>>>
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>> N Greve
>>> Sent: Thursday, October 12, 2017 4:16 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] cortical surface area
>>>
>>> mm2
>>>
>>>
>>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>>>> What measure is for the cortical surface area?
>>>>
>>>> The measure in the aparc.stats file states 'WhiteSurfArea'
>>>>
>>>> Jim
>>>>
>>>> 
>>>> -
>>>> -
>>>> --
>>>>
>>>> The materials in this message are private and may contain Protected
>>>> Healthcare Information or other information of a sensitive nature.
>>>> If you are not the intended recipient, be advised that any
>>>> unauthorized use, disclosure, copying or the taking of any action in
>>>> reliance on the contents of this information is strictly prohibited.
>>>> If you have received this email in error, please immediately notify
>>>> the sender via telephone or return mail.
>>>>
>>>>
>>>>
>>>> ___
>>>> 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

Re: [Freesurfer] cortical surface area

[Alexopoulos, Dimitrios]

Thanks.

I ran this command:
mris_anatomical_stats subjectID lh pial
It gave me a total surface area of 115007 mm^2

I also tried the following command from within the 'label' directory:
mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh pial
It gave me a total surface area 109458 mm^2

Which is the correct method and value for total cortical surface area?

Jim


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, October 12, 2017 5:17 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] cortical surface area

oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject
via:

mris_anatomical_stats   pial

cheers
Bruce
On Thu, 12 Oct 2017,
Alexopoulos, Dimitrios wrote:

> I don't see this file in the stats directory using FS 5.3.
>
> Jim
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
> Fischl
> Sent: Thursday, October 12, 2017 4:52 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] cortical surface area
>
> Hi Jim
>
> check the ?h.aparc.pial.stats file. I think the total surface area should be 
> in there.
>
> cheers
> Bruce
> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote:
>
>> Specifically, where in the aparc.stats file (or other file) is the cortical 
>> surface area?
>> I only see default output for  'WhiteSurfArea'.
>>
>> Jim
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>> N Greve
>> Sent: Thursday, October 12, 2017 4:16 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] cortical surface area
>>
>> mm2
>>
>>
>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>>>
>>> What measure is for the cortical surface area?
>>>
>>> The measure in the aparc.stats file states 'WhiteSurfArea'
>>>
>>> Jim
>>>
>>> 
>>> -
>>> -
>>> --
>>>
>>> The materials in this message are private and may contain Protected
>>> Healthcare Information or other information of a sensitive nature.
>>> If you are not the intended recipient, be advised that any
>>> unauthorized use, disclosure, copying or the taking of any action in
>>> reliance on the contents of this information is strictly prohibited.
>>> If you have received this email in error, please immediately notify
>>> the sender via telephone or return mail.
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>>
>> 
>> The materials in this message are private and may contain Protected 
>> Healthcare Information or other information of a sensitive nature. If you 
>> are not the intended recipient, be advised that any unauthorized use, 
>> disclosure, copying or the taking of any action in reliance on the contents 
>> of this information is strictly prohibited. If you have received this email 
>> in error, please immediately notify the sender via telephone or return mail.
>>
>> 

Re: [Freesurfer] cortical surface area

[Bruce Fischl]

oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject 
via:

mris_anatomical_stats   pial

cheers
Bruce
On Thu, 12 Oct 2017, 
Alexopoulos, Dimitrios wrote:

> I don't see this file in the stats directory using FS 5.3.
>
> Jim
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, October 12, 2017 4:52 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] cortical surface area
>
> Hi Jim
>
> check the ?h.aparc.pial.stats file. I think the total surface area should be 
> in there.
>
> cheers
> Bruce
> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote:
>
>> Specifically, where in the aparc.stats file (or other file) is the cortical 
>> surface area?
>> I only see default output for  'WhiteSurfArea'.
>>
>> Jim
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Thursday, October 12, 2017 4:16 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] cortical surface area
>>
>> mm2
>>
>>
>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>>>
>>> What measure is for the cortical surface area?
>>>
>>> The measure in the aparc.stats file states 'WhiteSurfArea'
>>>
>>> Jim
>>>
>>> -
>>> -
>>> --
>>>
>>> The materials in this message are private and may contain Protected
>>> Healthcare Information or other information of a sensitive nature. If
>>> you are not the intended recipient, be advised that any unauthorized
>>> use, disclosure, copying or the taking of any action in reliance on
>>> the contents of this information is strictly prohibited. If you have
>>> received this email in error, please immediately notify the sender
>>> via telephone or return mail.
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>>
>> 
>> The materials in this message are private and may contain Protected 
>> Healthcare Information or other information of a sensitive nature. If you 
>> are not the intended recipient, be advised that any unauthorized use, 
>> disclosure, copying or the taking of any action in reliance on the contents 
>> of this information is strictly prohibited. If you have received this email 
>> in error, please immediately notify the sender via telephone or return 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
>
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return 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] cortical surface area

[Alexopoulos, Dimitrios]

I don't see this file in the stats directory using FS 5.3.

Jim

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, October 12, 2017 4:52 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] cortical surface area

Hi Jim

check the ?h.aparc.pial.stats file. I think the total surface area should be in 
there.

cheers
Bruce
On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote:

> Specifically, where in the aparc.stats file (or other file) is the cortical 
> surface area?
> I only see default output for  'WhiteSurfArea'.
>
> Jim
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
> Greve
> Sent: Thursday, October 12, 2017 4:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] cortical surface area
>
> mm2
>
>
> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>>
>> What measure is for the cortical surface area?
>>
>> The measure in the aparc.stats file states 'WhiteSurfArea'
>>
>> Jim
>>
>> -
>> -
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If
>> you are not the intended recipient, be advised that any unauthorized
>> use, disclosure, copying or the taking of any action in reliance on
>> the contents of this information is strictly prohibited. If you have
>> received this email in error, please immediately notify the sender
>> via telephone or return mail.
>>
>>
>>
>> ___
>> 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.
>
>
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return 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


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cortical surface area

[Bruce Fischl]

Hi Jim

check the ?h.aparc.pial.stats file. I think the total surface area should 
be in there.

cheers
Bruce
On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote:

> Specifically, where in the aparc.stats file (or other file) is the cortical 
> surface area?
> I only see default output for  'WhiteSurfArea'.
>
> Jim
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, October 12, 2017 4:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] cortical surface area
>
> mm2
>
>
> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>>
>> What measure is for the cortical surface area?
>>
>> The measure in the aparc.stats file states 'WhiteSurfArea'
>>
>> Jim
>>
>> --
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If
>> you are not the intended recipient, be advised that any unauthorized
>> use, disclosure, copying or the taking of any action in reliance on
>> the contents of this information is strictly prohibited. If you have
>> received this email in error, please immediately notify the sender via
>> telephone or return mail.
>>
>>
>>
>> ___
>> 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.
>
>
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return 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] cortical surface area

[Alexopoulos, Dimitrios]

Specifically, where in the aparc.stats file (or other file) is the cortical 
surface area?
I only see default output for  'WhiteSurfArea'.

Jim


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Thursday, October 12, 2017 4:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical surface area

mm2


On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>
> What measure is for the cortical surface area?
>
> The measure in the aparc.stats file states 'WhiteSurfArea'
>
> Jim
>
> --
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
>
>
>
> ___
> 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.



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cortical surface area

[Douglas N Greve]

mm2


On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>
> What measure is for the cortical surface area?
>
> The measure in the aparc.stats file states ‘WhiteSurfArea’
>
> Jim
>
> 
>
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying or the taking of any action in reliance on 
> the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
>
>
>
> ___
> 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.

Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

[Emma Thompson]

This helps immensely, thank you!

On Tue, Oct 14, 2014 at 4:52 AM, Anderson M. Winkler  wrote:

> Hi Emma,
>
> Please, see below:
>
> On 13 October 2014 20:11, Emma Thompson  wrote:
>
>> Hi Anderson,
>> Thank you for your paper. I guess I am confused. I have analyzed my
>> structural data with qdec, specifically looking at a measure of cortical
>> thickness and volume. I'm considering looking at surface area as well but
>> was told it wasn't a very good measure using qdec, I have no other
>> information really. Could you speak to whether or not this measure is valid
>> in so far as one runs it using qdec?
>>
>
>
> The data that is used in qdec comes from mris_preproc, which uses
> vertexwise interpolation with Jacobian correction for local
> stretches/shrinkages. The amount of area is preserved globally, which is
> desirable, although locally it's something difficult to achieve. If without
> any smoothing, the spatial correlation between mris_preproc and the method
> in the paper is about 0.65, and the correlation at a given vertex, across
> subjects, varies spatially. Note, however, that the smoothing -- that is
> applied by default -- should increase the correlation vastly, but I don't
> have the exact numbers at hand to provide yet.
>
> For area, as well as for volume, the method shown in the paper is really
> the gold standard: it's pycnophylactic and thus guarantees that the amount
> of area is preserved locally everywhere in the brain during the
> interpolation. It's the same method used in GIS applications for
> geoprocessing. The downside is that the current implementation, using
> Matlab, is too slow (for the ico7, it can well take 10-15h per hemisphere
> in a single CPU).
>
>
>
>
>> Also, in your opinion, would it be redundant to look at surface area in
>> addition to measures of cortical thickness and cortical volume?
>>
>
>
> Actually, the redundant bit here is volume. Area and thickness are
> uncorrelated phenotypically and genetically, and each provide different
> pieces of information (this is shown here
>  and here
> ).
> Volume is a mixture of both, in proportions that vary across the cortical
> mantle. I would not consider using volume given that thickness and area are
> available. Moreover, volume is also an "areal quantity" in the sense that
> it requires the same methods for interpolation as surface area itself, so
> all that is said above about area applies also to cortical volumes.
>
> Hope this helps!
>
> All the best,
>
> Anderson
>
>
>
>
>
> On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler <
> wink...@fmrib.ox.ac.uk> wrote:
>
>> Hi Donna,
>>
>> In that same paper we also comment on the differences between
>> expansion/contraction and absolute areal measurements assessed at each face
>> of the surface (i.e., facewise), which can, after interpolation, be
>> converted to vertexwise to facilitate analysis using current tools (e.g.,
>> mri_glmfit or qdec), without loss of areal quantities.
>>
>> All the best,
>>
>> Anderson
>>
>>
>> On 11 October 2014 04:05, Donna Dierker  wrote:
>>
>>> Hi Emma,
>>>
>>> I might not be the only one who is unsure what you mean by a vertex-wise
>>> cortical surface area measure.  Do you mean something like what is
>>> illustrated in figures 2 and 3 here:
>>>
>>> http://www.pnas.org/content/107/29/13135.figures-only
>>>
>>> … which is similar, but not identical to the local gyrification index?
>>>
>>> If so, would you use this measure on surfaces before or after
>>> registration to a target atlas?
>>>
>>> Donna
>>>
>>>
>>> On Oct 10, 2014, at 4:19 PM, Emma Thompson 
>>> wrote:
>>>
>>> > Dear Freesurfers,
>>> > I recently heard that there are several disadvantages to using a
>>> measure of cortical surface area in Freesurfer, specifically due to
>>> conducting a vertex-wise analysis. Can someone help me understand why a
>>> measure of surface area using this approach might be flawed? Thanks!
>>>
>>>
>>>
>>> ___
>>> 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
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this

Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

[Douglas N Greve]

If you are using --qcache, then there is nothing wrong specifically with 
the qdec implementation

On 10/13/2014 03:11 PM, Emma Thompson wrote:
> Hi Anderson,
> Thank you for your paper. I guess I am confused. I have analyzed my 
> structural data with qdec, specifically looking at a measure of 
> cortical thickness and volume. I'm considering looking at surface area 
> as well but was told it wasn't a very good measure using qdec, I have 
> no other information really. Could you speak to whether or not this 
> measure is valid in so far as one runs it using qdec?
>
> Also, in your opinion, would it be redundant to look at surface area 
> in addition to measures of cortical thickness and cortical volume?
>
> Thanks for your help and apologizes for my silly questions.
>
> On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler 
> mailto:wink...@fmrib.ox.ac.uk>> wrote:
>
> Hi Donna,
>
> In that same paper we also comment on the differences between
> expansion/contraction and absolute areal measurements assessed at
> each face of the surface (i.e., facewise), which can, after
> interpolation, be converted to vertexwise to facilitate analysis
> using current tools (e.g., mri_glmfit or qdec), without loss of
> areal quantities.
>
> All the best,
>
> Anderson
>
>
> On 11 October 2014 04:05, Donna Dierker  > wrote:
>
> Hi Emma,
>
> I might not be the only one who is unsure what you mean by a
> vertex-wise cortical surface area measure. Do you mean
> something like what is illustrated in figures 2 and 3 here:
>
> http://www.pnas.org/content/107/29/13135.figures-only
>
> … which is similar, but not identical to the local
> gyrification index?
>
> If so, would you use this measure on surfaces before or after
> registration to a target atlas?
>
> Donna
>
>
> On Oct 10, 2014, at 4:19 PM, Emma Thompson
> mailto:vonecono...@gmail.com>> wrote:
>
> > Dear Freesurfers,
> > I recently heard that there are several disadvantages to
> using a measure of cortical surface area in Freesurfer,
> specifically due to conducting a vertex-wise analysis. Can
> someone help me understand why a measure of surface area using
> this approach might be flawed? Thanks!
>
>
>
> ___
> 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
>
>
> 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

-- 
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

Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

[Anderson M. Winkler]

Hi Emma,

Please, see below:

On 13 October 2014 20:11, Emma Thompson  wrote:

> Hi Anderson,
> Thank you for your paper. I guess I am confused. I have analyzed my
> structural data with qdec, specifically looking at a measure of cortical
> thickness and volume. I'm considering looking at surface area as well but
> was told it wasn't a very good measure using qdec, I have no other
> information really. Could you speak to whether or not this measure is valid
> in so far as one runs it using qdec?
>


The data that is used in qdec comes from mris_preproc, which uses
vertexwise interpolation with Jacobian correction for local
stretches/shrinkages. The amount of area is preserved globally, which is
desirable, although locally it's something difficult to achieve. If without
any smoothing, the spatial correlation between mris_preproc and the method
in the paper is about 0.65, and the correlation at a given vertex, across
subjects, varies spatially. Note, however, that the smoothing -- that is
applied by default -- should increase the correlation vastly, but I don't
have the exact numbers at hand to provide yet.

For area, as well as for volume, the method shown in the paper is really
the gold standard: it's pycnophylactic and thus guarantees that the amount
of area is preserved locally everywhere in the brain during the
interpolation. It's the same method used in GIS applications for
geoprocessing. The downside is that the current implementation, using
Matlab, is too slow (for the ico7, it can well take 10-15h per hemisphere
in a single CPU).




> Also, in your opinion, would it be redundant to look at surface area in
> addition to measures of cortical thickness and cortical volume?
>


Actually, the redundant bit here is volume. Area and thickness are
uncorrelated phenotypically and genetically, and each provide different
pieces of information (this is shown here
 and here
).
Volume is a mixture of both, in proportions that vary across the cortical
mantle. I would not consider using volume given that thickness and area are
available. Moreover, volume is also an "areal quantity" in the sense that
it requires the same methods for interpolation as surface area itself, so
all that is said above about area applies also to cortical volumes.

Hope this helps!

All the best,

Anderson





On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler  wrote:

> Hi Donna,
>
> In that same paper we also comment on the differences between
> expansion/contraction and absolute areal measurements assessed at each face
> of the surface (i.e., facewise), which can, after interpolation, be
> converted to vertexwise to facilitate analysis using current tools (e.g.,
> mri_glmfit or qdec), without loss of areal quantities.
>
> All the best,
>
> Anderson
>
>
> On 11 October 2014 04:05, Donna Dierker  wrote:
>
>> Hi Emma,
>>
>> I might not be the only one who is unsure what you mean by a vertex-wise
>> cortical surface area measure.  Do you mean something like what is
>> illustrated in figures 2 and 3 here:
>>
>> http://www.pnas.org/content/107/29/13135.figures-only
>>
>> ... which is similar, but not identical to the local gyrification index?
>>
>> If so, would you use this measure on surfaces before or after
>> registration to a target atlas?
>>
>> Donna
>>
>>
>> On Oct 10, 2014, at 4:19 PM, Emma Thompson  wrote:
>>
>> > Dear Freesurfers,
>> > I recently heard that there are several disadvantages to using a
>> measure of cortical surface area in Freesurfer, specifically due to
>> conducting a vertex-wise analysis. Can someone help me understand why a
>> measure of surface area using this approach might be flawed? Thanks!
>>
>>
>>
>> ___
>> 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
>
>
> 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

Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

[Emma Thompson]

Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my
structural data with qdec, specifically looking at a measure of cortical
thickness and volume. I'm considering looking at surface area as well but
was told it wasn't a very good measure using qdec, I have no other
information really. Could you speak to whether or not this measure is valid
in so far as one runs it using qdec?

Also, in your opinion, would it be redundant to look at surface area in
addition to measures of cortical thickness and cortical volume?

Thanks for your help and apologizes for my silly questions.

On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler  wrote:

> Hi Donna,
>
> In that same paper we also comment on the differences between
> expansion/contraction and absolute areal measurements assessed at each face
> of the surface (i.e., facewise), which can, after interpolation, be
> converted to vertexwise to facilitate analysis using current tools (e.g.,
> mri_glmfit or qdec), without loss of areal quantities.
>
> All the best,
>
> Anderson
>
>
> On 11 October 2014 04:05, Donna Dierker  wrote:
>
>> Hi Emma,
>>
>> I might not be the only one who is unsure what you mean by a vertex-wise
>> cortical surface area measure.  Do you mean something like what is
>> illustrated in figures 2 and 3 here:
>>
>> http://www.pnas.org/content/107/29/13135.figures-only
>>
>> … which is similar, but not identical to the local gyrification index?
>>
>> If so, would you use this measure on surfaces before or after
>> registration to a target atlas?
>>
>> Donna
>>
>>
>> On Oct 10, 2014, at 4:19 PM, Emma Thompson  wrote:
>>
>> > Dear Freesurfers,
>> > I recently heard that there are several disadvantages to using a
>> measure of cortical surface area in Freesurfer, specifically due to
>> conducting a vertex-wise analysis. Can someone help me understand why a
>> measure of surface area using this approach might be flawed? Thanks!
>>
>>
>>
>> ___
>> 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
>
>
> 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


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] cortical surface area measurement and vertex-wise analysis

[Anderson M. Winkler]

Hi Donna,

In that same paper we also comment on the differences between
expansion/contraction and absolute areal measurements assessed at each face
of the surface (i.e., facewise), which can, after interpolation, be
converted to vertexwise to facilitate analysis using current tools (e.g.,
mri_glmfit or qdec), without loss of areal quantities.

All the best,

Anderson


On 11 October 2014 04:05, Donna Dierker  wrote:

> Hi Emma,
>
> I might not be the only one who is unsure what you mean by a vertex-wise
> cortical surface area measure.  Do you mean something like what is
> illustrated in figures 2 and 3 here:
>
> http://www.pnas.org/content/107/29/13135.figures-only
>
> ... which is similar, but not identical to the local gyrification index?
>
> If so, would you use this measure on surfaces before or after registration
> to a target atlas?
>
> Donna
>
>
> On Oct 10, 2014, at 4:19 PM, Emma Thompson  wrote:
>
> > Dear Freesurfers,
> > I recently heard that there are several disadvantages to using a measure
> of cortical surface area in Freesurfer, specifically due to conducting a
> vertex-wise analysis. Can someone help me understand why a measure of
> surface area using this approach might be flawed? Thanks!
>
>
>
> ___
> 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


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] cortical surface area measurement and vertex-wise analysis

[Anderson M. Winkler]

Hi Emma,

Could you clarify what would be the disadvantages that you've heard about?
I ask because we've studied and tried to clarify many aspects of the
analysis of surface area in this paper
. Maybe
if there's something not covered there we could try to comment then.

Thanks!

All the best,

Anderson


On 10 October 2014 22:19, Emma Thompson  wrote:

> Dear Freesurfers,
> I recently heard that there are several disadvantages to using a measure
> of cortical surface area in Freesurfer, specifically due to conducting a
> vertex-wise analysis. Can someone help me understand why a measure of
> surface area using this approach might be flawed? Thanks!
>
> ___
> 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


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] cortical surface area measurement and vertex-wise analysis

[Donna Dierker]

Hi Emma,

I might not be the only one who is unsure what you mean by a vertex-wise 
cortical surface area measure.  Do you mean something like what is illustrated 
in figures 2 and 3 here:

http://www.pnas.org/content/107/29/13135.figures-only

… which is similar, but not identical to the local gyrification index?

If so, would you use this measure on surfaces before or after registration to a 
target atlas?

Donna


On Oct 10, 2014, at 4:19 PM, Emma Thompson  wrote:

> Dear Freesurfers,
> I recently heard that there are several disadvantages to using a measure of 
> cortical surface area in Freesurfer, specifically due to conducting a 
> vertex-wise analysis. Can someone help me understand why a measure of surface 
> area using this approach might be flawed? Thanks!



___
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.

Re: [Freesurfer] cortical surface area related measures

[j janssen]

Regarding Winkler et al.:

http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/
On Aug 21, 2012 11:00 PM, "Gregory Kirk"  wrote:

>
> Hi folks, I wanted to make sure i have everything straight w.r.t. the
> surface area measures.
>
> as i see there are 4 ways implemented ( somewhere ) to do cortical surface
> area analysis.
>
> 1. areal expansion
>
> 2. Local Gyrification Index
>
> 3. direct vertex based true surface area glm, Winkler AM et. al
>
> 4. roi based, i.e. based on the surface areas of the parcellation units in
> lh.aparc.a2009s.stats etc.
>
>
> 1. recent pub, Lisa T. Eyler et. al used the areal expansion method.
> was this done exactly as would be achived by using the area tab on qdec
> and setting up a glm ?
> Dale published surface area specifying some details of implementation but
> i was not sure
> if this was exactly what is implemented in qdec ?
>
> 2. LGI seems to me this is the ratio of two areas, that of the hull to the
> area inscribed by projecting
> the border of the hull onto the grey/white surface. In an e-mail Nick said
> LGI is a curvature based measure and that
> confused me a bit. gyrification is of course related to curvature but it
> seems the quantities actually calculated here are ratios of areas, which
> gives local info on surface area differences.
>
> 3. the winkler stuff is i think not publicly available yet at this time ?
>
> 4. straightforward enough not withstanding ICV corrections, etc.
>
> any words of clarification before i start trying some analysis on my group
> ?
>
> thank you
>
> Greg
> ___
> 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


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] cortical surface area related measures

[Douglas N Greve]

Hi Greg, I don't know what "areal expansion" refers to. If you want to 
use area (eg, the area tab in qdec), you should make sure to download 
the most recent version of mris_preproc (which performs a jacobian type 
correction)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
doug


On 08/21/2012 04:59 PM, Gregory Kirk wrote:
> Hi folks, I wanted to make sure i have everything straight w.r.t. the surface 
> area measures.
>
> as i see there are 4 ways implemented ( somewhere ) to do cortical surface
> area analysis.
>
> 1. areal expansion
>
> 2. Local Gyrification Index
>
> 3. direct vertex based true surface area glm, Winkler AM et. al
>
> 4. roi based, i.e. based on the surface areas of the parcellation units in 
> lh.aparc.a2009s.stats etc.
>
>
> 1. recent pub, Lisa T. Eyler et. al used the areal expansion method.
> was this done exactly as would be achived by using the area tab on qdec and 
> setting up a glm ?
> Dale published surface area specifying some details of implementation but i 
> was not sure
> if this was exactly what is implemented in qdec ?
>
> 2. LGI seems to me this is the ratio of two areas, that of the hull to the 
> area inscribed by projecting
> the border of the hull onto the grey/white surface. In an e-mail Nick said 
> LGI is a curvature based measure and that
> confused me a bit. gyrification is of course related to curvature but it 
> seems the quantities actually calculated here are ratios of areas, which 
> gives local info on surface area differences.
>
> 3. the winkler stuff is i think not publicly available yet at this time ?
>
> 4. straightforward enough not withstanding ICV corrections, etc.
>
> any words of clarification before i start trying some analysis on my group ?
>
> thank you
>
> Greg
> ___
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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.