Hi there!
Since this is my first time using FreeSurfer, I found it quite challenging
to get the handle on the different coordinate systems used. My goal is to
generate vtk files where the vtk cortical surface and the vtk fiber tracts
are in the same space (for one individual subject).
Basically,
Hi all,
Is using forced permutation for non-orthogonal design matrices wrong or is it
allowed to do this instead of using tools like palm (what happens eg with the
covariates when using forced permutation)? I used forced permutation and it
seemed to work, results were (partly) comparable to w
Hello all,
I am wondering why results would change completely for between group volume
analysis when using demeaned/mean-centered ICV compared to using ICV as a
covariate in mri_glmfit? See the figures below.
Does demeaning the covariate inherently change the results comapred to the
raw covariate
do you mean the ones that are between the two surfaces? You could use
mris_fill to fill the interior of the white then use it as a mask in
mri_mask
cheers
Bruce
On Sun, 28 Aug 2016, Fire Tech wrote:
Dear all
I am searching for a solution to remove wm.mgz voxels which are enclosed by
pial
Hi Woo-Suk
why not just do the surface analysis that they are requesting? I'm not
sure what you are asking, but certainly volume = surface area * thickness
in general, and so a volumetric effect can be driven by one or both of
surface area and thickness
cheers
Bruce
On
Sat, 27 Aug 2016, Wo
not sure what you are testing, but if you are, eg, looking at the
difference between two groups regressing out ICV, then it can make a
huge difference
On 08/29/2016 12:36 PM, Corinna Bauer wrote:
> Hello all,
>
> I am wondering why results would change completely for between group
> volume ana
Sorry for not specifying. Yes, we are looking at difference in volume
between the two groups using DODS. What is the most statistically sound...
raw values, demeaning across the entire sample, or demeaning with groups
separately? FYI, I exported the ICV values to SAS and there is a
significant diff
If there was not an interaction between group and ICV, I would say to
use DOSS where demeaning does not make a difference. Since there is an
interaction, you have to use DODS, but the interpretation is no longer
easy. If you do not demean, then you are implictly testing for a
difference at ICV=
Yes, I agree completely. We are using DODS and it is clear that we have
different results depending on which type of ICV we use. The question is...
which type of ICV correction for DODS is the most statistically sound?
demean across all groups, no demeaning, or demean within groups separately.
Wha
You definitely do not want to demean within group. Having said that, no
demeaning method is more "sound" than the other. The problem is in the
interpretation. Imagaine you have a plot of volume vs ICV for each
group. When you have an interaction, the best-fit lines will intersect
at some ICV. I
On 29 August 2016 at 02:24, Knut J Bjuland wrote:
> Is it possible to use a script to extract information about which library
> that is used for each recons?Or are there any other means to get this
> information?
I'm not sure about that. At least some of the info is recorded as part
of the o
It is hard to say. Since the subjects are not exchangeable, the
permutation is technically not appropriate. Check the winkler paper, I
think he talks about what happens if you just don't do anything.
On 08/29/2016 11:07 AM, maaike rive wrote:
>
> Hi all,
>
>
> Is using forced permutation for n
Hi Maaike,
Why not just use PALM? Then you don’t have to worry about this (since
PALM appropriately handles the situation of correlated covariates).
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disor
Does PALM do surface-based? Also, there is no way to appropriately
handle this. For permutation, non-orthogonal designs are wrong. There
are ways to try to compensate for it, which is what PALM is doing. Sorry
to be nit-picky!
On 08/29/2016 06:12 PM, Harms, Michael wrote:
> Hi Maaike,
> Why no
PALM handles GIFTI and CIFTI data.
Peace,
Matt.
On 8/29/16, 6:21 PM, "Douglas N Greve"
wrote:
>Does PALM do surface-based? Also, there is no way to appropriately
>handle this. For permutation, non-orthogonal designs are wrong. There
>are ways to try to compensate for it, which is what PALM is
Hi,
I wouldn’t say that non-orthogonal designs are “wrong” to use with
permutation. Rather, there are different approaches to handling that
situation and produce approximate p-values. See Table 2 in Winkler’s 2014
paper, and the results therein comparing the various approaches:
http://www.ncbi.
Hi Huasheng,
Here you go:
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip
I am also cc-ing the freesurfer list.
--Thomas
On Tue, Aug 30, 2016 at 11:05 AM, liuhas_20040125
wrote:
> Dear professor Yeo :
>
>
>
> My name is Huasheng Liu, I'm from central
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