Hi Jay,
your command and design files seem fine.
Matt has the feeling that the tfce correction might make the whole thing stall. This might be for various reasons, one of which being a wrong subject ordering. Are you absolutely sure to have concatenated your subjects in GM_mod_merg in the same order as you assume they are in the design.mat? In other words, if you've run VBM with all the default settings, it will have concatenated the subjects in the alphabetical order, which then MUST correspond to the design.mat ordering.
In any case, even if you feel that the order is right, could you please re-run randomise with --debug and let us know the outcome?
Cheers,
Gwenaelle
--- En date de : Jeu 15.4.10, Jay Ives <[log in to unmask]> a écrit :
De: Jay Ives <[log in to unmask]>
Objet: [FSL]
À: [log in to unmask]
Date: Jeudi 15 avril 2010, 11h15
Hi Gwenaelle,
Here are the design files. The command I used was
randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t design.con -T -n 5000 -V
Thanks for the help.
J
----- Original Message -----
From: Gwenaëlle
DOUAUD
To: [log in to unmask]
Sent: Tuesday, April 13, 2010 6:52 PM
Subject: Re: [FSL] FSLVBM GLM Setup
Hi Jay,
this should not take that long... There
might be indeed something wrong in your design or the set up of your
contrasts (though just showing them separately is not saying that much to
us).
Could you please attach the design.mat and .con as well as the
command you've typed to run
randomise?
Cheers,
Gwenaelle
--- En date de : Mar
13.4.10, Jay Ives <[log in to unmask]> a écrit :
De:
Jay Ives <[log in to unmask]>
Objet: Re: [FSL] FSLVBM GLM
Setup
À: [log in to unmask]
Date: Mardi 13 avril 2010,
0h48
Hi Gwenaëlle (and Mark),
I did use your
method 2, but thought I got it wrong because randomise stalled at
iteration 2! I gave it overnight, but no progress.
With 70 subjects
in 4 groups (of different sizes), is this expected to take a long time?
It might have taken forever...
Thx
J
On Tue Apr 13 2:20 , Gwenaëlle DOUAUD
sent:
Hi
Mark and Jay,
there is no good answer to this question I'm
afraid.
Say you've got two subjects in group A, 3 in B and 4
in C, then both approaches are valid:
Method I
A
B
1 0
1 0
0 1
0 1
0 1
for the design.mat of the
first A and B groups with
1 -1 (A-B)
-1 1 (B-A)
for the
design.con
and then repeat for groups B and C, then groups A and C
(which is what you did Mark).
Method II
A B C
1 0
0
1 0 0
0 1 0
0 1 0
0 1 0
0 0 1
0 0 1
0 0 1
0
0 1
for the design.mat of the 3 groups with
1 -1 0
(A-B)
-1 1 0 (B-A)
0 1 -1 (B-C)
0 -1 1 (C-B)
1 0 -1
(A-C)
-1 0 1 (C-A)
for the design.con (t-tests)
and
1
0 1 0 0 0
for the design.fts (F-test, as many columns as there are
rows in your design.con, you just need to click in "F-tests" in the
Glm gui and then click in front of the two relevant "Contrasts" you
have already set up)
So with Method II, you can also ask the
question of where are the changes *across the 3 groups* (F-test with
the design.fts). You also get an increase in DoF but, as Tom Nichols
said, if it happens that group C for instance has wildly smaller
variance, you can get inflated significances (or reduced power if it
has wildly larger variance).
So it depends on what your main
question is, really.
Hope this helps,
Gwenaelle
--- En date de : Lun 12.4.10, Mark Walterfang <[log in to unmask]> a
écrit :
> De: Mark Walterfang <[log in to unmask]>
> Objet: Re:
[FSL] FSLVBM GLM Setup
> À: [log in to unmask]
> Date: Lundi 12 avril 2010,
14h18
> Hi all
>
> I'm in the same situation as
Jay. I have three groups
> (illness1, illness2
> and
controls), all matched to each other. I've run three
> two-way
analyses,
> which is pretty laborious and I'm pretty sure it's
not
> statistically ideal.
> What I can't work out is how
to set up the design matrices
> & contrasts in
> the
way Jay describes, as the online manual for Randomise
> doesn't
really
> provide guidance here. Gwenaëlle, is this something
you
> can advise on?
>
> Thanks in advance,
>
> Mark Walterfang
>
>
> On 10/4/10 12:29
PM, "Jay Ives" <[log in to unmask]>
>
wrote:
>
> > I have 70 subjects in 4 groups and would
like to test
> between individual
> > groups and
combinations of the groups. Can someone
> please advise me how
to set
> > up the design.mat and design.con files to do
this?
> Thx
>
>
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