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/
>>
>> ___
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is 
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>> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent 
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>>
>>
>> 
>> The materials in this message are private and may contain Protected 
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>> are not the intended recipient, be advised that any unauthorized use, 
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>> of this information is strictly prohibited. If you have received this email 
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> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 

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.
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
> 
> 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.
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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.
>
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>
>
>
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The materials in this message are private and may contain Protected Healthcare 
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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.
>
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> Freesurfer mailing list
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>
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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/

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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.



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 
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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/

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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
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Re: [Freesurfer] volume vs surface-based and surface smoothing

[Douglas N Greve]

The surface is created during recon-all. rawfunc2surf-sess resamples the 
volumetric fMRI onto the surface.


On 10/12/2017 01:42 PM, Alissa Stafford wrote:
> Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?
>
> From:  > on behalf of Matt 
> Glasser >
> Reply-To: Freesurfer support list  >
> Date: Thursday, October 12, 2017 at 1:39 PM
> To: Freesurfer support list  >
> Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing
>
> Volume-based registration is fine with subject as you have the same 
> brain that you are registering (ideally such registrations are 6 DOF 
> rigid registrations and any image distortions are corrected for). 
>  Surface-based registration is better when comparing across subjects 
> due to the variability in cortical folding patterns and locations of 
> areas relative to folds across subjects.  Smoothing is best done on 
> the surface if it is done at all.  Smoothing in the volume harms one’s 
> spatial localization precision much more than smoothing on the surface 
> for an equivalent FWMH in mm.  It is worth keeping in mind that 
> smoothing on the surface does still blur across cortical areal 
> boundaries, however, so for many analyses it may be better to average 
> within cortical areas rather than to smooth a lot.
>
> Peace,
>
> Matt.
>
> From:  > on behalf of Alissa 
> Stafford >
> Reply-To: Freesurfer support list  >
> Date: Thursday, October 12, 2017 at 12:29 PM
> To: "Freesurfer@nmr.mgh.harvard.edu 
> " 
> >
> Subject: [Freesurfer] volume vs surface-based and surface smoothing
>
> Hello,
>
> I am trying to understand the preprocessing functions to successfully 
> complete surface-based analysis. I am confused about what is happening 
> on the volume level and when exactly the surface is being created. My 
> questions revolve around register-sess and rawfunc2surf-sess.
>
> Registration has 2 parts:
> 1: the native anatomical space is registered with the fsaverage space. 
> This is happening during recon-all.
> 2: native functional data is registered with the native anatomical 
> data. This is happening during register-sess in preprocess-sess.
> Aren’t these both volume-based registrations? If not when are the 
> surfaces created? My concern is that it is volume-based and I was 
> under the impression from this article: 
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all 
> registrations should be done on the surface.
>
> I am also confused about rawfunc2surf-sess. I believe up until this 
> function in preprocess-sess, everything has been done in the volume so 
> this is the first step that is done in the surface, is that correct? 
> And then does this do smoothing? I realized it has a fwhm input option 
> so it must smooth. So is this where the functional data is now 
> expressed in the surface and it also smooths? Or does surfsmooth-sess 
> need to be run in addition to rawfunc2surf-sess?
>
> I basically just want to be making sure I understand when registration 
> is volume-based or surface-based and when it’s appropriate to use 
> volume-based. And I was using the rawfunc2surf function assuming it 
> was for smoothing, but I am not so sure if this only creates the 
> surface or also smooths.
>
> Thanks,
> Alissa
> ___ Freesurfer mailing 
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-- 
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

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

[stdp82]

I have applied the contrasts that we discussed in the previous mails but they 
produce doubt results.

In summary, I aim to look at:
A- Difference between groups without considerer the covariate effect (I 
suppose that the maps will be in the intercept folder) --->  ANOVA between 4 
groups
B- Clusters in which the fMRI (dependent variable) is associated to the 
structural data (covariate), taking in account the groups (I suppose that the 
maps will be in the slope folder) --->  MANOVA between 4 groups

Please could you check the contrast reported below? I suspect that there are 
some errors because, looking at results: 
The slope map is the inverse in color of the intercept map and the intercept 
did not correspond to the results which I obtain by using G4V0

C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0
C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25
C15) group.effect.intercept
1 -1 0 0 0 0 0 0
1 0 -1 0 0 0 0 0
1 0 0 -1 0 0 0 0
C16) group.effect.slope
0 0 0 0 1 -1 0 0
0 0 0 0 1 0 -1 0
0 0 0 0 1 0 0 -1

Best regards


Stefano


>Messaggio originale
>Da: "Douglas N Greve" 
>Data: 11-ott-2017 17.28
>A: , 
>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of 
covariance
>
>the rational is to make them sum to 1.0 so that the gamma.mgh file has 
>units of mm (or whatever the input units are). It is unimportant for 
>p-values.
>
>
>On 10/10/2017 01:54 PM, std...@virgilio.it wrote:
>> Thanks
>>
>> In which contrast I must change "1" with "0.25"?
>> What is the rationale to use 0.25?
>>
>>
>> Sent from Virgilio Mobile
>> 
>>
>> Il 10/10/2017, Douglas N Greve  ha scritto:
>>
>> I don't understand what you mean by "where I should use"
>>
>> I thought I looked through all those contrasts a few weeks ago, no?
>>
>>
>> On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
>>> You have suggested to use
>>> 0 0 0 0 .25 .25 .25 .25
>>> to look the map where, considering the group differences, the covariate
>>> predicts the dependent variable (functional connectivity) in 4GV1.
>>>
>>> Below I'm reporting the contrast that I have used.
>>> Please could you check it and suggest correction?
>>> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?
>>>
>>> Thanks
>>>
>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>>> C15) group.effect.intercept
>>> 1 -1 0 0 0 0 0 0
>>> 1 0 -1 0 0 0 0 0
>>> 1 0 0 -1 0 0 0 0
>>> C16) group.effect.slope
 0 0 0 0 1 -1 0 0
 0 0 0 0 1 0 -1 0
 0 0 0 0 1 0 0 -1
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
 Thank you very much.
 Where I should put 0 0 0 0 .25 .25 .25 .25?
 Which are the contrast reported below that I should modify?

 C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
 C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
 C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
 C15) group.effect.intercept
 1 -1 0 0 0 0 0 0
 1 0 -1 0 0 0 0 0
 1 0 0 -1 0 0 0 0
 C16) group.effect.slope
 0 0 0 0 1 -1 0 0
 0 0 0 0 1 0 -1 0
 0 0 0 0 1 0 0 -1
 Messaggio originale
 Da: "Douglas Greve" 
 Data: 9-ott-2017 22.56
 A: 
 Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance

 I don't know what you are asking


 On 10/6/17 9:24 AM, 

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

[stdp82]

I have applied the contrasts that we discussed in the previous mails but they 
produce doubt results.

In summary, I aim to look at:
A- Difference between groups without considerer the covariate effect (I 
suppose that the maps will be in the intercept folder) --->  ANOVA between 4 
groups
B- Clusters in which the fMRI (dependent variable) is associated to the 
structural data (covariate), taking in account the groups (I suppose that the 
maps will be in the slope folder) --->  MANOVA between 4 groups

Please could you check the contrast reported below? I suspect that there are 
some errors because, looking at results: 
1- The slope map is the inverse in color of the intercept map.
2- Newly, I would to verify whether the fcMRI difference observed between 
groups are associated to change in covariate (volume).

C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0
 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25
C15) group.effect.intercept
1 -1 0 0 0 0 0 0
1 0 -1 0 0 0 0 0
1 0 0 -1 0 0 0 0
C16) group.effect.slope
0 0 0 0 1 -1 0 0
0 0 0 0 1 0 -1 0
0 0 0 0 1 0 0 -1

Best regards


Stefano

>Messaggio originale
>Da: "Douglas N Greve" 
>Data: 11-ott-2017 17.28
>A: , 
>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of 
covariance
>
>the rational is to make them sum to 1.0 so that the gamma.mgh file has 
>units of mm (or whatever the input units are). It is unimportant for 
>p-values.
>
>
>On 10/10/2017 01:54 PM, std...@virgilio.it wrote:
>> Thanks
>>
>> In which contrast I must change "1" with "0.25"?
>> What is the rationale to use 0.25?
>>
>>
>> Sent from Virgilio Mobile
>> 
>>
>> Il 10/10/2017, Douglas N Greve  ha scritto:
>>
>> I don't understand what you mean by "where I should use"
>>
>> I thought I looked through all those contrasts a few weeks ago, no?
>>
>>
>> On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
>>> You have suggested to use
>>> 0 0 0 0 .25 .25 .25 .25
>>> to look the map where, considering the group differences, the covariate
>>> predicts the dependent variable (functional connectivity) in 4GV1.
>>>
>>> Below I'm reporting the contrast that I have used.
>>> Please could you check it and suggest correction?
>>> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?
>>>
>>> Thanks
>>>
>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>>> C15) group.effect.intercept
>>> 1 -1 0 0 0 0 0 0
>>> 1 0 -1 0 0 0 0 0
>>> 1 0 0 -1 0 0 0 0
>>> C16) group.effect.slope
 0 0 0 0 1 -1 0 0
 0 0 0 0 1 0 -1 0
 0 0 0 0 1 0 0 -1
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
 Thank you very much.
 Where I should put 0 0 0 0 .25 .25 .25 .25?
 Which are the contrast reported below that I should modify?

 C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
 C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
 C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
 C15) group.effect.intercept
 1 -1 0 0 0 0 0 0
 1 0 -1 0 0 0 0 0
 1 0 0 -1 0 0 0 0
 C16) group.effect.slope
 0 0 0 0 1 -1 0 0
 0 0 0 0 1 0 -1 0
 0 0 0 0 1 0 0 -1
 Messaggio originale
 Da: "Douglas Greve" 
 Data: 9-ott-2017 22.56
 A: 
 Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance

 I don't know 

[Freesurfer] cortical surface area

[Alexopoulos, Dimitrios]

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 
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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
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Re: [Freesurfer] volume vs surface-based and surface smoothing

[Matt Glasser]

My understanding of the FreeSurfer surface-based functional processing is
that it adheres to the below guidelines; however, I have not personally used
it so we¹ll have to see what the FreeSurfer experts say.

Peace,

Matt.

From:   on behalf of Alissa Stafford

Reply-To:  Freesurfer support list 
Date:  Thursday, October 12, 2017 at 12:42 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] volume vs surface-based and surface smoothing

Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?

From:  on behalf of Matt Glasser

Reply-To: Freesurfer support list 
Date: Thursday, October 12, 2017 at 1:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From:  on behalf of Alissa Stafford

Reply-To: Freesurfer support list 
Date: Thursday, October 12, 2017 at 12:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
___ Freesurfer mailing list
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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
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___ Freesurfer mailing list
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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] volume vs surface-based and surface smoothing

[Alissa Stafford]

Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?

From: 
>
 on behalf of Matt Glasser >
Reply-To: Freesurfer support list 
>
Date: Thursday, October 12, 2017 at 1:39 PM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain that 
you are registering (ideally such registrations are 6 DOF rigid registrations 
and any image distortions are corrected for).  Surface-based registration is 
better when comparing across subjects due to the variability in cortical 
folding patterns and locations of areas relative to folds across subjects.  
Smoothing is best done on the surface if it is done at all.  Smoothing in the 
volume harms one’s spatial localization precision much more than smoothing on 
the surface for an equivalent FWMH in mm.  It is worth keeping in mind that 
smoothing on the surface does still blur across cortical areal boundaries, 
however, so for many analyses it may be better to average within cortical areas 
rather than to smooth a lot.

Peace,

Matt.

From: 
>
 on behalf of Alissa Stafford 
>
Reply-To: Freesurfer support list 
>
Date: Thursday, October 12, 2017 at 12:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully complete 
surface-based analysis. I am confused about what is happening on the volume 
level and when exactly the surface is being created. My questions revolve 
around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This is 
happening during recon-all.
2: native functional data is registered with the native anatomical data. This 
is happening during register-sess in preprocess-sess.
Aren’t these both volume-based registrations? If not when are the surfaces 
created? My concern is that it is volume-based and I was under the impression 
from this article:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , 
that all registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function in 
preprocess-sess, everything has been done in the volume so this is the first 
step that is done in the surface, is that correct? And then does this do 
smoothing? I realized it has a fwhm input option so it must smooth. So is this 
where the functional data is now expressed in the surface and it also smooths? 
Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is 
volume-based or surface-based and when it’s appropriate to use volume-based. 
And I was using the rawfunc2surf function assuming it was for smoothing, but I 
am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
___ Freesurfer mailing list 
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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


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] volume vs surface-based and surface smoothing

[Matt Glasser]

Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From:   on behalf of Alissa Stafford

Reply-To:  Freesurfer support list 
Date:  Thursday, October 12, 2017 at 12:29 PM
To:  "Freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
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[Freesurfer] volume vs surface-based and surface smoothing

[Alissa Stafford]

Hello,

I am trying to understand the preprocessing functions to successfully complete 
surface-based analysis. I am confused about what is happening on the volume 
level and when exactly the surface is being created. My questions revolve 
around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This is 
happening during recon-all.
2: native functional data is registered with the native anatomical data. This 
is happening during register-sess in preprocess-sess.
Aren’t these both volume-based registrations? If not when are the surfaces 
created? My concern is that it is volume-based and I was under the impression 
from this article:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , 
that all registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function in 
preprocess-sess, everything has been done in the volume so this is the first 
step that is done in the surface, is that correct? And then does this do 
smoothing? I realized it has a fwhm input option so it must smooth. So is this 
where the functional data is now expressed in the surface and it also smooths? 
Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is 
volume-based or surface-based and when it’s appropriate to use volume-based. 
And I was using the rawfunc2surf function assuming it was for smoothing, but I 
am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
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[Freesurfer] dcmunpack

[Keiko McCreary]

Hi There,

Could someone tell me how long approximately dcmunpack should take? (I have
243 files and it has been "interrogating" now for 2 hours.

Thank you!

Keiko

-- 
J. Keiko McCreary, PhD
Postdoctoral Fellow
SARTAN-AD Clinical Research Coordinator  (Lethbridge Site)
Canadian Centre for Behavioural Neuroscience
University of Lethbridge
Office: EP 1218
Phone: 403-394-3985 Cell: 403-393-0181
keiko.mccrea...@uleth.ca or @gmail.com
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Re: [Freesurfer] Normalize to mni

[Elijah Mak]

Hi Jan,

Is the functional image already coregistered to the T1? If you have a 
registration file, you could try:

mri_vol2vol --mov fstcmc.nii.gz --reg registrationfile --tal --talres 2 --o 
fstcmc.mni305.2mm.nii.gz

.. to bring the functional image to MNI305. Are you planning to your restrict 
your analysis (assuming it is a voxelwise analysis?) to the subcortical 
regions? You could use the subcort.mask.mgz in fsaverage/mri.2mm as as mask in 
your mri_glmfit.

I will leave it to Doug to confirm if those steps are suitable for your 
objectives.

Best Wishes,
Elijah 


Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


> On 12 Oct 2017, at 16:14, Jan Willem Koten  wrote:
> 
> Normalize to mni
>  
> Dear Doug,
>  
> We have a very simple question. In a first step we segmented brains using the 
> recon all command. Our functional pipeline created a „fstcmc.nii.gz“ file. We 
> would like to do some subcortical analysis and need to perfrorm this in MNI 
> 305 space. We also need the subcortical labels for the actual analysis 
> itself. Does someone know the trick? In short how do we get from 
> fstcmc.nii.gz“ to subcortical functional ROI's?
>  
> Greetings Jan
> Jan Willem Koten (van Grevenbicht)
> 
> Zollernstrasse 57, 52070 Aachen, Germany
> Telephone: (0049) (0)241 212 44
>  
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[Freesurfer] Normalize to mni

[Jan Willem Koten]

Normalize to mni

 

Dear Doug,

 

We have a very simple question. In a first step we segmented brains using the recon all command. Our functional pipeline created a „fstcmc.nii.gz“ file. We would like to do some subcortical analysis and need to perfrorm this in MNI 305 space. We also need the subcortical labels for the actual analysis itself. Does someone know the trick? In short how do we get from fstcmc.nii.gz“ to subcortical functional ROI's?

 

Greetings Jan


Jan Willem Koten (van Grevenbicht)

Zollernstrasse 57, 52070 Aachen, Germany
Telephone: (0049) (0)241 212 44

 
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Re: [Freesurfer] Problem flipping a label into other hemisphere

[Neuro Lists]

Hi Doug and Bruce,
I forgot to mention that I had tried that as well but without success. As a
sanity check, tried flipping a label from the 'bert' subject and it still
comes out wrong. I've uploaded a screen shot of the result:

https://imgur.com/a/J6Phx

Thank you for any input you might have!

These were the exact steps the following (I also tried playing around with
the options to --streg but without luck):

cd ${SUBJECTS_DIR}/bert
cd surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
cd ../label

mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
../surf/lh.sphere.left_right ../surf/rh.sphere


$Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $

cwd /home/joe/subjects/bert/label

cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg
lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere

sysname  Linux

hostname computer

machine  x86_64

user joe

srcvalfile  (null)

trgvalfile  lh_flip.BA45.label

nsurfs  2

jac  0

revmap  0

1 Loading ../surf/lh.sphere.left_right

2 Loading ../surf/rh.sphere

Loading label lh.BA45.label

   4060 points in input label

MRISapplyReg: nsurfs = 2, revmap=0, jac=0,  hash=1

MRISapplyReg: building hash tables (res=16).

MRISapplyReg: Forward Loop (133299)

MRISapplyReg: Dividing by number of hits (133299)

MRISapplyReg: nSrcLost = 38462

   4505 points in output label

mris_apply_reg done





On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve 
wrote:

> Try
>
> mris_apply_reg --src-label your.lh.label --trg your.rh.label  -streg
> lh.sphere.left_right rh.sphere
>
> On 10/11/17 5:43 PM, Neuro Lists wrote:
>
> Hi all,
> I've searched the lists extensively and have not been able to resolve my
> problem. I'd greatly appreciated any help.
>
> I have run the recon-all pipeline on a number of subjects, made the
> appropriate fixes and am happy with the surfaces. For each subject, I have
> a number of ROIs that are created programmatically and they are exactly as
> they should be. These ROIs are on the "regular" surfaces, not the inflated
> ones. In other words, opening the brainmask.mgz in freeview and just
> loading the label file results in the ROI being where I expect it to be.
>
>
>  I'm now trying to flip the ROI onto the contralateral hemisphere and this
> is going terribly wrong. No matter what I try, the ROI ends up being
> generated far outside of the brain.
>
>
> I was originally trying to use the xhemi pipeline, but then I realized
> from the forums that I could just use mris_left_right_register.
>
> I've done:
>
> cd subject/surf
> mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
> rh.sphere.left_right
>
> I've then tried using a number of varieties of mri_apply_reg that have
> been listed on the forum:
> 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label  -streg
> lh.sphere lh.sphere.left_right
> 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right
> rh.sphere.left_right --trg rh.lh.source.label
>
>
> No matter what I try though, the flipped ROI ends up being way outside of
> the brain when I overlay it on the brainmask. Is this because the flipped
> ROI should instead be visualized on the inflated hemisphere? If so, how can
> I get it to overlay properly onto the brainmask so that I can be sure it's
> correct? My ultimate goal is to get anatomical stats from the original and
> flipped ROIs.
>
>
> Thanks for your help!
>
> Joe
>
>
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