On 2/19/2022 6:10 PM, fernanda rohrsetzer wrote:
External Email - Use Caution
Hi guys,
I'm a beginner in Freesurfer and I want to perform an analysis of the
difference between 3 groups in cortical thickness,volume and area
having age, mean thickness and etiv as covariate.
my design
External Email - Use Caution
Hi guys,
I'm a beginner in Freesurfer and I want to perform an analysis of the
difference
between 3 groups in cortical thickness,volume and area having age, mean
thickness and etiv as covariate.
my design matrix for 3 groups
comparison as "1 -1 0 0
More covariates follows the same pattern as having one or two coviariates
On 11/20/17 9:18 PM, 박경일 wrote:
Dear experts,
I am trying to perform mri_glmfit to generate images indicating
cortical thickness differences between groups. My data has 6 or 7
covariates such age, sex, smoking,
Dear experts,
I am trying to perform mri_glmfit to generate images indicating cortical
thickness differences between groups. My data has 6 or 7 covariates such age,
sex, smoking, hypertension, diabetes etc.
I wonder how to make contrasts.mat files.Those are supposed to be a lot of
files.
Dear experts,
I am trying to perform mri_glmfit to generate images indicating cortical
thickness differences between groups. My data has 6 or 7 covariates such
age, sex, smoking, hypertension, diabetes etc.
I wonder how to make contrasts.mat files.Those are supposed to be a lot of
files.
The F would be
1 -1 0 0
0 0 -1 0
Your t-contrasts are correct (you don't need to do both directions)
On 08/03/2015 03:40 PM, Lim, Lena wrote:
Hi experts,
I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file,
how should I define the F contrast? Would it still be: I -1 0
Hi experts,
I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file, how
should I define the F contrast? Would it still be: I -1 0 ?
Got it! I guess we may work around by specifying weighted contrast like [ 0.1
0.2 0.3 0.4 ] ?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
On 2/18/14 11:25 PM, Douglas Greve
Dear FreeSurfer experts,
I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV),
and 1 nuisance factor (NUI). I want to make sense of some specification of the
regressors and contrasts.
Because they are not described in
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I
That looks right to me
doug
On 02/18/2014 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer experts,
I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate
(COV), and 1 nuisance factor (NUI). I want to make sense of some
specification of the regressors and contrasts.
Because
Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would
the effect be biased toward large sample sizes in one of the groups (versus the
other groups)?
Or, does FreeSurfer qdec take care of the unequal cell, in a possible way
analogous to using Type III SS in the
It will tend to weight smaller groups by a proportion greater than the
number of subjects in the group.
On 02/18/2014 01:58 PM, Yang, Daniel wrote:
Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25
0.25], would the effect be biased toward large sample sizes in one of
Doug, sorry, I am not sure I can fully understand.
Do you mean the results are weighted MORE toward groups with smaller sample
sizes (than groups with larger sample sizes)?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail:
Let's say you have four groups with 10 20 30 40 (100 total). The first
group would get a weight of .25 where it only had 10% of the total. I
don't think there is any way around this.
On 2/18/14 4:07 PM, Yang, Daniel wrote:
Doug, sorry, I am not sure I can fully understand.
Do you mean the
Hi,
I am trying to figure out the contrasts to use for a study. I am comparing
age matched patients and controls (all female). The FSGD file has 4
columns, but I'm not sure how to make an appropriate contrast matrix. Any
guidance would be appreciated. I can't seem to find an applicable example
on
Both of those will essentially test the same thing, just with a
different sign. FS always computes two-tailed tests and reports both
tails, so the sign is only a matter of convention. Assuming the Patient
class is first in the FSGD and you want volunteers patients to show up
as yellow, then
Hi Doug,
Our hypothesis is that cortical thickness will be lower in patients than in
volunteers, once controlled for gender, age, education, etc. I may remove
MMSE as diagnosis of the patient is in part based on the MMSE scores. In
that case, I would have 12 regressors, in the order you listed
In this case you have 4 class variables and 3 continuous, so you'll have
16 regressors (and so 16 elements in your contrast). Your actual
contrast vector depends on the order of your class variables in the
fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors
will have the
Linda Zhang wrote:
Hi Doug,
Thanks for the clarification. If I were to add another two class
variables (patient and subject, for example) and I wanted to see if
they affected thickness, assuming they come after gender in the fsgd
file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0
Hi Doug,
Sure, my fsgd file contained two groups originally, M and F. I had three
continuous variables, which were Age, MMSE, Education. I wanted to test
whether thickness is correlated with MMSE scores after controlling for
gender, age and education. I now want to add two more class variables
Dear all,
I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is
that correct?) but I've come across an error when trying to do the next
step in the tutorial.
I didn't cache the data during recon-all, so I ran the following:
mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage
Hi Linda, you have two class varibles (M and F) and three continuous
variables (Age, MMSE, and ED), so you'll have 2*(3+1)=8 regressors, so
your contrast will have 6 elements. The order of the elements will be:
1. M-offset
2. F-offset
3. M-AgeSlope
4. F-AgeSlope
5. M-MMSE-Slope
6. F-MMSE-Slope
does /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh
exist?
doug
Linda Zhang wrote:
Dear all,
I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0
0]...is that correct?) but I've come across an error when trying to do
the next step in the tutorial.
I
Dear all,
I have a bit of an amateur question. I've read the slides and tutorial for
group analysis, but I'm still confused about the contrasts. I made my fsgd
file, which contains two groups: M and F. I also have three continuous
variables: Age, MMSE, Education. I would like to test whether
I want to run a GLM DODS in Freesurfer to test whether patients differ from
controls with regard to cortical thickness, meanwhile I want to control for
several variables, both discrete as continues.
This is my manually made fsgd file
GroupDescriptorFile 1
Title fsgd pat con.txt
Hi Petra, you have mixed up a class with the level of a factor (an easy
thing to do). From your FSGD, it looks like you would need 8 classes,
each class would be a combination of a level from each factor. So one
class would be control-male-adni, etc. Once you have a proper FSGD file,
the 1st contrast looks correct. I'm not sure what you're trying to do
with the 2nd contrast. This would be a test for g1g2 on the 3rd
covariate (essentially an interaction between g1/g2 and the 3rd cov). It
would not be a post-hoc test because that's not the test you did in the
first contrast.
...@nmr.mgh.harvard.edu
Fecha: Martes, 11 de Enero de 2011, 17:01
Asunto: Re: [Freesurfer] contrasts using DODS
A: Jose Luis Cantero Lorente jlcan...@upo.es
CC: Freesurfer mailing list freesurfer@nmr.mgh.harvard.edu
the 1st contrast looks correct. I'm not sure what you're trying
to do
with the 2nd contrast
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