Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

[Duran, Tugce]

I tried that and I got an error in the Mask function that excludes the 
inter-hemispheric cut in matlab.

It doesn’t like the lh/rh.pial surfaces of the fsaverage.



This is the code:



0001 function mask = SurfStatMaskCut( surf );

0002

0003 %Mask that excludes the inter-hemisphere cut.

0004 %

0005 % Usage: mask = SurfStatMaskCut( surf );

0006 %

0007 % surf.coord   = 3 x v matrix of surface coordinates, v=#vertices.

0008 %

0009 % mask = 1 x v vector, 1=inside, 0=outside, v=#vertices.

0010 %

0011 % It looks in -50thresh,

0012 % where thresh = 1.5 x arg max of a histogram of |x|.

0013

0014 f=(abs(surf.coord(2,:))<50 ...

0015 & abs(surf.coord(3,:)-10)<30 ...

0016 & abs(surf.coord(1,:))<3);

0017 b=(0:0.02:3);

0018 h=hist(abs(surf.coord(1,f)),b);

0019 t=b(find(h==max(h)))*1.5;

0020 mask=~(abs(surf.coord(1,:)) wrote:



You can map it onto fsaverage, which is made only from 40 subjects, so

there is a little more folding





On 01/09/2018 06:27 PM, Duran, Tugce wrote:

> Total N is 159. I have min # of 52 subjects for certain analyses. I used 
avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and 
thickness data.

> Can the visualization issue be fixed?

>

> Thanks!

> Tugce

>

> dur...@iupui.edu

>

> On 1/9/18, 6:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

>

>  This is not entirely unexpected as the volume-based average of pial

>  surfaces will lose folds as you add subjects. How many subjects do 
you

>  have? Note that this is only a visualization issue if all your

>  underlying analysis is done on the surface.

>

>

>  On 01/08/2018 01:14 PM, Duran, Tugce wrote:

>  >

>  > Hi FS experts,

>  >

>  > I’m running SurfStat on my freesurfer skullstriped data (recon-all

>  > with –noskullstrip flag) and getting pecan shaped brain images as

>  > shown in the attached file.

>  >

>  > Do you know what freesurfer process (make_average_subject or glm or

>  > other)  is causing this issue?

>  >

>  > Thanks!

>  >

>  > *Tugce Duran, B.S.*

>  >

>  > /Research Technologist II/

>  >

>  > cid:image001.png@01D3861A.789F16C0

>  > 

>  >

>  > Indiana Alzheimer Disease Center (iADC)

>  >

>  > Office: 317-278-7015

>  >

>  > dur...@iupui.edu 

>  >

>  >

>  >

>  > ___

>  > 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 
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and properly

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>

>

>

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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

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

[Douglas N Greve]

You can map it onto fsaverage, which is made only from 40 subjects, so 
there is a little more folding


On 01/09/2018 06:27 PM, Duran, Tugce wrote:
> Total N is 159. I have min # of 52 subjects for certain analyses. I used 
> avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and 
> thickness data.
> Can the visualization issue be fixed?
>
> Thanks!
> Tugce
>
> dur...@iupui.edu
>
> On 1/9/18, 6:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Douglas N Greve"  gr...@nmr.mgh.harvard.edu> wrote:
>
>  This is not entirely unexpected as the volume-based average of pial
>  surfaces will lose folds as you add subjects. How many subjects do you
>  have? Note that this is only a visualization issue if all your
>  underlying analysis is done on the surface.
>  
>  
>  On 01/08/2018 01:14 PM, Duran, Tugce wrote:
>  >
>  > Hi FS experts,
>  >
>  > I’m running SurfStat on my freesurfer skullstriped data (recon-all
>  > with –noskullstrip flag) and getting pecan shaped brain images as
>  > shown in the attached file.
>  >
>  > Do you know what freesurfer process (make_average_subject or glm or
>  > other)  is causing this issue?
>  >
>  > Thanks!
>  >
>  > *Tugce Duran, B.S.*
>  >
>  > /Research Technologist II/
>  >
>  > cid:image001.png@01D3861A.789F16C0
>  > 
>  >
>  > Indiana Alzheimer Disease Center (iADC)
>  >
>  > Office: 317-278-7015
>  >
>  > dur...@iupui.edu 
>  >
>  >
>  >
>  > ___
>  > Freesurfer mailing list
>  > Freesurfer@nmr.mgh.harvard.edu
>  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  
>  --
>  Douglas N. Greve, Ph.D.
>  MGH-NMR Center
>  gr...@nmr.mgh.harvard.edu
>  Phone Number: 617-724-2358
>  Fax: 617-726-7422
>  
>  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>  Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>  
>  ___
>  Freesurfer mailing list
>  Freesurfer@nmr.mgh.harvard.edu
>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  
>  
>  The information in this e-mail is intended only for the person to whom 
> it is
>  addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
>  contains patient information, please contact the Partners Compliance 
> HelpLine at
>  http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
>  but does not contain patient information, please contact the sender and 
> properly
>  dispose of the e-mail.
>  
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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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Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

[Duran, Tugce]

Total N is 159. I have min # of 52 subjects for certain analyses. I used 
avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and 
thickness data.
Can the visualization issue be fixed? 

Thanks!
Tugce

dur...@iupui.edu

On 1/9/18, 6:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

This is not entirely unexpected as the volume-based average of pial 
surfaces will lose folds as you add subjects. How many subjects do you 
have? Note that this is only a visualization issue if all your 
underlying analysis is done on the surface.


On 01/08/2018 01:14 PM, Duran, Tugce wrote:
>
> Hi FS experts,
>
> I’m running SurfStat on my freesurfer skullstriped data (recon-all 
> with –noskullstrip flag) and getting pecan shaped brain images as 
> shown in the attached file.
>
> Do you know what freesurfer process (make_average_subject or glm or 
> other)  is causing this issue?
>
> Thanks!
>
> *Tugce Duran, B.S.*
>
> /Research Technologist II/
>
> cid:image001.png@01D3861A.789F16C0 
> 
>
> Indiana Alzheimer Disease Center (iADC)
>
> Office: 317-278-7015
>
> dur...@iupui.edu 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the 
e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in 
error
but does not contain patient information, please contact the sender and 
properly
dispose of the e-mail.



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Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

[Douglas N Greve]

This is not entirely unexpected as the volume-based average of pial 
surfaces will lose folds as you add subjects. How many subjects do you 
have? Note that this is only a visualization issue if all your 
underlying analysis is done on the surface.


On 01/08/2018 01:14 PM, Duran, Tugce wrote:
>
> Hi FS experts,
>
> I’m running SurfStat on my freesurfer skullstriped data (recon-all 
> with –noskullstrip flag) and getting pecan shaped brain images as 
> shown in the attached file.
>
> Do you know what freesurfer process (make_average_subject or glm or 
> other)  is causing this issue?
>
> Thanks!
>
> *Tugce Duran, B.S.*
>
> /Research Technologist II/
>
> cid:image001.png@01D3861A.789F16C0 
> 
>
> Indiana Alzheimer Disease Center (iADC)
>
> Office: 317-278-7015
>
> dur...@iupui.edu 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.