If you're referring to VERTEX-WISE analyses of area and volume, there
are "issues" with the interpretability of those measures.
Don Hagler has posted on this several times.
For example, most recently see:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15205.html
cheers,
-MH
On Tu
Hi Mira,
If the map you provided is of uncorrected p-values at say p=0.05, then
you appear to have just a couple small regions of group differences, so
it isn't surprising that after FDR nothing would survive.
The result is what it is, and unless you had specific a priori
hypotheses regarding re
Hi Ed,
Is there a distinction in FreeSurfer between "cortical" and
"subcortical" white matter? I thought that white matter was simply
white matter...
You wrote that the white matter values in aseg.stats are identical to
the output of mris_wm_volume, which is exactly what I would expect.
You do
Yes, I think that using average cortical thickness is a reasonable
covariate to use in thickness analyses. And total cortical surface area
likewise if you are analyzing regional surface areas, although in the
case of surface area you need to decide whether to use areas based on
the GM or WM surfa
t each
region's thickness by its proportion of the total surface area.
cheers,
-MH
On Thu, 2010-12-16 at 11:57 -0600, Michael Harms wrote:
> Yes, I think that using average cortical thickness is a reasonable
> covariate to use in thickness analyses. And total cortical surface area
>
con3
> >
> >
> > BTW: You can't "sum" the thicknesses across the various regions in
> the
> > aparc files, as that would be a meaningless measure. You either need
> to
> > compute the average cortical thickness as I suggested, or compute a
> > w
Creating a custom label and then using mris_anatomical_stats is probably
the route I would go as well. But out of curiosity, if I was combining
whole labels (and not splitting or subdividing any of them) I'd also
compute an "average" thickness weighted by the mid-thickness surface
area -- the two
Hi Gergely,
Was this collected on a Siemens scanner? If so, the Siemen's MPRAGE
sequence is such that the "slices" form the "inner loop" of the
acquisition -- that is "Number of slices" lines in k-space are acquired
for each TR period. So, having a differing number of slices theoretically
has an
Hi Justin,
It partly depends on what exactly you want when you say "brain volume".
Do you want a measure of estimated intracranial volume (intended to be
independent of atrophy)? A measure of gray matter + white matter +
ventricles? Or only gray matter + white matter? Do you care whether
the ce
It really is just a matter of justifying and explaining your chosen
statistical model. If you believe that two groups have the same
regression slope for a parameter (but possibly different
offsets/intercepts), then you would use a "DOSS" model -- this is akin
to a model in SPSS/SAS in which you m
Hi Rita,
I would not automatically assume that regarding slice ordering with
"interleaved" acquisitions, as I don't think that there is necessarily
any "standard" that different manufacturers are committed to following.
It is actually a non-trivial issue -- e.g., how do scanner choices
regarding a
Hi Chris,
There really shouldn't be a "thickness-age correlation group difference"
result with the DOSS model. I have FS 4.1 (rather than 5.0 on my
system) but running an analogous model, I see that I do indeed get a
verbal "Description" for such a contrast. However, if I compare that to
the "th
subjects.
> >
> > One last aside. The demeaning of covariates still slightly confuses
> > me. In a DOSS model it seems it wouldn't matter where you measure
> > the intercept since both ageXthickness slopes are equal. In the DODS
> > model, it doesn't seem
How about using mris_volume to get the volume of everything enclosed
within the pial surface, and then subtracting out the volume of the
ventricles as represented in the aseg? We have used that approach to
define a measure of "total brain volume".
Best,
-MH
On Tue, 2011-03-22 at 14:36 -0400, An
See the usage statement for 'mris_anatomical_stats' below -- just end
your command with the surface name (i.e., pial).
Also, you don't need the -t flag (lh.pial is not a thickness file, and
thickness is independent of whether stats are computed on the 'white'
vs. 'pial' surface).
usage: mris_ana
Freesurfer's estimate of ICV ("eTIV") is designed to be insensitive to
brain atrophy -- after all, it is an estimate of "intracranial volume",
not brain volume. See the Buckner et al. (2004) paper for a validation
of this.
cheers,
-MH
On Fri, 2011-04-08 at 17:04 -0500, Gonzalo Rojas Costa wrote
Hi Gallen,
I suggest that you extract the values across subjects at a single vertex
in fsaverage space, and then attempt to duplicate FS's uncorrected t-
and p-values at that vertex with your SPSS model. Those HAVE to be
identical if you are truly using the same model (unless there is an
unknown
Hi Cleo,
See the following page created by Jeanette Mumford for a helpful
exposition of how mean centering affects your data:
http://mumford.fmripower.org/mean_centering/
As for your DOSS model, there is a "bug" in how QDEC describes the
contrasts in that case. See the following posts:
http://
ilto:gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, May 04, 2011 3:42 PM
> To: Gallen, Courtney (NIH/NIDA) [F]
> Cc: Michael Harms; Freesurfer Mailing List
> Subject: Re: [Freesurfer] Interpreting results from Qdec
>
> You can edit the label by hand to only include one vertex. If y
anks again for your continued help!
> Courtney
>
> -Original Message-
> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, May 04, 2011 3:42 PM
> To: Gallen, Courtney (NIH/NIDA) [F]
> Cc: Michael Harms; Freesurfer Mailing List
> Subject: Re: [Freesurfer]
Hi Fernanda,
The choice between ICV vs a measure of total "brain volume" or total
cortical gray matter volume depends on whether you want to control for
potential overall brain atrophy. Using ICV will control for overall
"head size", but not for potential overall brain atrophy (e.g., with
age, or
I continue using the ICV?
>
> Thanks again,
>
>
> On Tue, May 17, 2011 at 9:57 AM, Michael Harms
> wrote:
>
> Hi Fernanda,
> The choice between ICV vs a measure of total "brain volume" or
> total
> cortica
interpolation in the generation of the mri/orig.mgz, which brings with
it blurring (i.e., the same sort of concerns that prompt one to use a
single MPRAGE, rather than the average of two MPRAGEs)
Just curious...
thanks,
-MH
--
Michael Harms, Ph.D.
--
Just as an FYI, we also recently encountered the same problem, also
using mri_convert as our DICOM to NIFTI converter. Our work-around was
to just switch to dcm2nii.
Jolinda: I don't know why mri_convert is populating a "slice_code" entry
for a Siemens MPRAGE acquisition, since an MPRAGE is a
on of the slices so
> that we could always depend on voxel coordinates having some anatomical
> meaning, regardless of what crazy slice orientation was prescribed. Not
> sure if Doug has some easier work around for you to prevent the rotation.
>
> cheers
> Bruce
>
>
>
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