Re: [Freesurfer] comparison of mean thickness of gyri in two groups
Thank you for your suggestions Bruce and Mike. Mike, could you please provide the motivation behind your suggestion of using mean cortical thickness as a covariate ? Let's consider this is the context of a simple example. Let's say we compare the mean thickness of the pre-central gyrus in patients versus controls. Does the biology suggest that even after one accounts for age and gender, there are natural variations in the gyrus thickness measurements ( that is, some people would just happen to have larger thickness measurements ) ? If this is the case, then one could normalize the thickness of the individual gyrus measurement (pre-central gyrus in this example) with the mean cortical thickness. However, in most of the papers I have only seen age and gender used as co-variates. Thanks Mehul On Sun, Nov 1, 2009 at 4:44 PM, Michael Harms wrote: > > To me, it makes much more sense to use mean cortical thickness as a > covariate for thickness-based analyses. > > cheers, > Mike H. > > > Hi Mehul, > > > > the MNI group had an abstract showing that thickness didn't need eTIV > > correction at HBM a number of years ago, and it has been our experience > > as well. > > > > cheers, > > Bruce > > > > On Sat, 31 Oct 2009, Mehul Sampat wrote: > > > >> Hi Folks, > >> > >> If am comparing the mean thickness for certain gyri (pre-central, > >> post-central) in a controls versus patients. > >> I obtain the thickness measurements from lh.aparc.a2009s.stats and > >> rh.aparc.a2009s.stats > >> I was wondering if I need to normalize these thickness measurement > >> with the estimated > >> total intracranial volume (eTIV) ? > >> > >> Or has anyone reported that the these are independent of eTIV ? If so > >> then > >> as I understand I would only > >> need to account for age and gender in any subsequent analysis using GLM. > >> > >> Thanks > >> Mehul > >> > > ___ > > 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] comparison of mean thickness of gyri in two groups
To me, it makes much more sense to use mean cortical thickness as a covariate for thickness-based analyses. cheers, Mike H. > Hi Mehul, > > the MNI group had an abstract showing that thickness didn't need eTIV > correction at HBM a number of years ago, and it has been our experience > as well. > > cheers, > Bruce > > On Sat, 31 Oct 2009, Mehul Sampat wrote: > >> Hi Folks, >> >> If am comparing the mean thickness for certain gyri (pre-central, >> post-central) in a controls versus patients. >> I obtain the thickness measurements from lh.aparc.a2009s.stats and >> rh.aparc.a2009s.stats >> I was wondering if I need to normalize these thickness measurement >> with the estimated >> total intracranial volume (eTIV) ? >> >> Or has anyone reported that the these are independent of eTIV ? If so >> then >> as I understand I would only >> need to account for age and gender in any subsequent analysis using GLM. >> >> Thanks >> Mehul >> > ___ > 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] Making nice images using FreeSurfer
Hi Estephan,
1. Can't you just save tiffs of each of the different views and put them
together in photoshop?
2. You can write tcl scripts to do this kind of thing. For example
make_movie.tcl:
read_binary_sulc
set min_p 0
set max_p 36
for {set pno $min_p } { $pno <= $max_p} {incr pno 1} {
redraw
set fname $hemi.angle${pno}[format "%04d" $pno].tif
save_tiff $fname
puts "finished saving tiff file $fname"
rotate_brain_y 10
}
exit
then run
tksurfer $subject $hemi inflated -tcl make_movie.tcl
cheers,
Bruce
On Sun, 1 Nov 2009, Estephan Moana wrote:
> Hello FreeSurfer experts,
>
> I am playing with displaying FEAT output over the 3D pial surface provided by
> FS. I was wondering if somebody knows how to:
>
> 1. See both hemispheres side-by-side at the same time (both pial and
> inflated, if possible);
> 2. Make a video of the output 3D brain rotating at a certain axis
> (x,y or z), and maybe transitioning from pial to inflated surface.
> This may not really matters for scientific purposes, but it should
> produce some "wows" during lectures and thesis defense (my goal).
> AFNI does it, but its rendering option makes the image grainy,
> resulting in a video with poor resolution.
>
> Thank you.
>
> Estephan Moana, DDS
> Graduate Student
> Oral Biology PhD Program - Neurobiology track
> School of Dentistry, UNC- Chapel Hill
> 2140 Old Dental Building, CB# 7455
> Chapel Hill, NC 27599
> Phone: (919) 966-5680 Fax: (919) 966-5339
> mo...@email.unc.edu
>
___
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[Freesurfer] Making nice images using FreeSurfer
Hello FreeSurfer experts, I am playing with displaying FEAT output over the 3D pial surface provided by FS. I was wondering if somebody knows how to: 1. See both hemispheres side-by-side at the same time (both pial and inflated, if possible); 2. Make a video of the output 3D brain rotating at a certain axis (x,y or z), and maybe transitioning from pial to inflated surface. This may not really matters for scientific purposes, but it should produce some "wows" during lectures and thesis defense (my goal). AFNI does it, but its rendering option makes the image grainy, resulting in a video with poor resolution. Thank you. Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 mo...@email.unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
