Folks:
I am (still!) trying to get traction on some aspects of the current FS coordinate system(s).
In the recon-all pipeline, am I right in assuming that from orig.mgz all the way through to aseg.mgz and then on to brain.mgz, wm.mgz and so on, that there's NO resampling to a new coordinate system (eg: the specific brain's data doesn't get resampled to rotate or talairach it)?
Ie: if you overlay, for example, wm.mgz's data onto orig.mgz, it'll align properly? (Ie: overlay the raw voxel data, unmolested by any clever viewer transforms...)
I *think* I'm right on this, but it's hard to be sure, because for example, mri_ca_normalize's docs say that it takes a gca transform file as input. But that *might* be so that mri_ca_normalize can resample some other standard file to match the specific brainmask.mgz file.
<scratching of head>
Graham
Hi Graham,
yes, they are all in the same coordinate system. mri_ca_register takes a transform to initialize the nonlinear atlas alignment, but everything is in the same voxel space at the end of the day.
cheers, Bruce On Tue, 12 Sep 2006, Graham Wideman wrote:
Folks:
I am (still!) trying to get traction on some aspects of the current FS coordinate system(s).
In the recon-all pipeline, am I right in assuming that from orig.mgz all the way through to aseg.mgz and then on to brain.mgz, wm.mgz and so on, that there's NO resampling to a new coordinate system (eg: the specific brain's data doesn't get resampled to rotate or talairach it)?
Ie: if you overlay, for example, wm.mgz's data onto orig.mgz, it'll align properly? (Ie: overlay the raw voxel data, unmolested by any clever viewer transforms...)
I *think* I'm right on this, but it's hard to be sure, because for example, mri_ca_normalize's docs say that it takes a gca transform file as input. But that *might* be so that mri_ca_normalize can resample some other standard file to match the specific brainmask.mgz file.
<scratching of head>
Graham
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Valentina
I created a statistical parametric map and I visualized it on tksurfer. I didn't use a variable and I used a contrast vector (1 -1) because I was interested in knowing the difference between two classes. I'd like to know how I can interpreter the two colors, in other words do the two different colors means that there is a difference two classes? (i.e. the thickness of the cortex is greater in class one than class two: color red; the thickness of the cortex is lower in class one than class two: color blue). Another question is: why I need to create an average subject? Just to visualize the surface or it is used for the statistical analysis somhow?
Thanks Valentina
Durastanti, Valentina (NIH/NINDS) [F] wrote:
Valentina
I created a statistical parametric map and I visualized it on tksurfer. I didn't use a variable and I used a contrast vector (1 -1) because I was interested in knowing the difference between two classes. I'd like to know how I can interpreter the two colors, in other words do the two different colors means that there is a difference two classes? (i.e. the thickness of the cortex is greater in class one than class two: color red; the thickness of the cortex is lower in class one than class two: color blue).
This interpretation is correct.
Another question is: why I need to create an average subject? Just to visualize the surface or it is used for the statistical analysis somhow?
It is mostly for display purposes, but it is also used to compute the number of nearest neighbor iterations from the FWHM when performing surface smoothing. But I think it won't make much of a difference.
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have another question about the statistical parametric map, which is the value of the p considered significant? Thanks Valentina
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 19, 2006 6:40 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Graham Wideman; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] visualization of statistical analysis
Durastanti, Valentina (NIH/NINDS) [F] wrote:
Valentina
I created a statistical parametric map and I visualized it on tksurfer. I didn't use a variable and I used a contrast vector (1 -1) because I was interested in knowing the difference between two classes. I'd like to know how I can interpreter the two colors, in other words do the two different colors means that there is a difference two classes? (i.e.
the
thickness of the cortex is greater in class one than class two: color red; the thickness of the cortex is lower in class one than class two: color blue).
This interpretation is correct.
Another question is: why I need to create an average subject? Just to visualize the surface or it is used for the statistical analysis
somhow?
It is mostly for display purposes, but it is also used to compute the number of nearest neighbor iterations from the FWHM when performing surface smoothing. But I think it won't make much of a difference.
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Durastanti, Valentina (NIH/NINDS) [F] -
Graham Wideman