Hello List,
I want to run an F-test on a ROI (I selected the voxels with some
criterion).
If I understand correctly the way to do it is by computing the F-statistic
using:
F=(roi_betas'*X'*M*X*roi_betas)/(Y'*R*Y)*(J-p)/p1
where:
roi_betas are the average beta values across the roi
X is the
Hi Bruce,
Thanks a lot for your reply.
2. The surface area of fsaverage is less than any individual, so you
*definitely* don't want to use it. You should map the ROI back to individuals
and compute it in the native space.
I have two follow-up questions:
1) Do .pial.avg.area.mgh and/or
Hi Michael,
sure. Partially it's because the way we generate fsaverage is a bit
simple-minded as it is only intended for visualization. Each vertex is the
average talairach coordinate at that point on the sphere. In general,
you can think of averaging as acting as a low-pass filter so that you
Hi Boris,
1. Doug can say for sure, but I believe so.
2. No. The mid surface doesn't correspond to any boundary in the image and
so we are always hesitant to provide any morphometric measures for it. We
are working on a more explicit estimation of the location of layer IV, but
that is a future
Ok, tried this out and things are still coming out a little bit odd.
I manually edited the label file to just include the peak vertex and then
re-ran mri_segstats on that label. When I look at these values in SPSS, things
are still not quite significant (p ~ 0.09).
Could this have anything to
Think in 2D about averaging two sine waves that are shifted 90 degrees
from one another.
The length of of the resulting line will be far less than that of either
curve.
On 05/11/2011 11:20 PM, Michael Waskom wrote:
Hi Bruce,
I've seen this brought up on the list a few times, and, I have to
Yes, the avg.area files have the average over the input subjects at each
vertex. I've used it to overcome this problem.
doug
On 5/12/11 8:04 AM, Bruce Fischl wrote:
Hi Boris,
1. Doug can say for sure, but I believe so.
2. No. The mid surface doesn't correspond to any boundary in the image
Dear all,
I'd like to analyse some Freesurfer outputs in Matlab. I know it is
possible to load ./surf/lh.thickness into Matlab using read_curv, but
is it also possible to load normalized (and smoothed) thickness maps,
i.e. thickness maps registered to fsaverage, for vertex-wise
comparison? I
Hi Courtney,
If the t/F stats that you are getting for a single vertex in Qdec do not
match what you get in SPSS when analyzing the same input data (up to a
trivial precision difference), then the odds are that whatever model you
are using in SPSS is not that same as that implemented in Qdec.
Also, just to make this explicit: I'd compare actual statistic (t or F)
values, since comparing p-value requires that you also account for one-
sided vs. two-sided statistical testing.
-MH
On Thu, 2011-05-12 at 09:22 -0400, Gallen, Courtney (NIH/NIDA) [F]
wrote:
Ok, tried this out and things
Hi Bruce and Doug,
thank you both so much for your help.
You could generate it yourself easily enough
though.
For now I am taking the geometric average between pial and white surface
coordinates.
Is that the right way to do it, or is there a more precise way?
Also: If I decided to
Hi Michelle,
those aren't necessarily problems. We see this in lower quality scans
where you get little 1d protruberances that have very small radius of
curvature. Have you checked the ?h.white surface in those locations? At the
end of the day, that's what you really care about. If you don't
I was invited to be co-author of a chapter of a new book on radiology. The
chapter is about neuro anatomy and the main author is interested in using the
images of the patients I have processed in FreeSurfer, to demonstrate the
anatomy of the sulcs and gyri, as well as brain structures. I
Hi Boris,
For now I am taking the geometric average between pial and white
surface coordinates.
Is that the right way to do it, or is there a more precise way?
To obtain a surface that lies in the geometric middle between white and
pial surfaces, it is correct to take the average of the
How do I stop receiving emails from everyone asking and responding to
questions about FreeSurfer?
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On Thu, 12 May 2011, Krista Kelly wrote:
How do I stop receiving emails from everyone asking and responding to
questions about FreeSurfer?
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Hi,
I have files from Siemen's Skyra which I have used MRI_Convert to nii
I have tried using just the dicom files as well as changing the files to
*.nii.gz but I still get the error
corRead(): can't open file
/home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info
$Id: mri_convert.c,v
can you send us the command line you are using?
Bruce
On Fri, 13 May 2011, Vanessa
Lim wrote:
Hi,
I have files from Siemen's Skyra which I have used MRI_Convert to nii
I have tried using just the dicom files as well as changing the files to
*.nii.gz but I still get the error
Hi Vanessa,
Is sparseg a directory? Try pointing it at one of the dcm files from that set .
Best Martin
On May 12, 2011, at 8:21 PM, Vanessa Lim v@auckland.ac.nz wrote:
Hi,
I have files from Siemen's Skyra which I have used MRI_Convert to nii
I have tried using just the dicom
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