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]https://medicine.iu.edu/departments/neurology/research/
Indiana Alzheimer Disease Center (iADC) Office: 317-278-7015 durant@iupui.edumailto:durant@iupui.edu
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 https://medicine.iu.edu/departments/neurology/research/
Indiana Alzheimer Disease Center (iADC)
Office: 317-278-7015
durant@iupui.edu mailto:durant@iupui.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
durant@iupui.edu
On 1/9/18, 6:19 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > https://medicine.iu.edu/departments/neurology/research/ > > Indiana Alzheimer Disease Center (iADC) > > Office: 317-278-7015 > > durant@iupui.edu mailto:durant@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 greve@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.
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
durant@iupui.edu
On 1/9/18, 6:19 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > <https://medicine.iu.edu/departments/neurology/research/> > > Indiana Alzheimer Disease Center (iADC) > > Office: 317-278-7015 > > durant@iupui.edu <mailto:durant@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 greve@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
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 -50<y<50 and -20<z<40, and mask vertices where |x|>thresh,
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,:))<t & f); %%% <---This is where the error occurs %%%
0021
0022 return
0023 end
On 1/9/18, 6:41 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> 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
>
> durant@iupui.edu
>
> On 1/9/18, 6:19 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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
> > https://medicine.iu.edu/departments/neurology/research/
> >
> > Indiana Alzheimer Disease Center (iADC)
> >
> > Office: 317-278-7015
> >
> > durant@iupui.edu mailto:durant@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
> greve@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
greve@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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Duran, Tugce