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FSL  December 2007

FSL December 2007

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Subject:

Re: FEAT-Higher level analysis, works with fixed-effects, but not mixed

From:

"Sen, Suman" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 19 Dec 2007 12:12:49 -0500

Content-Type:

text/plain

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text/plain (119 lines)

Hi Steve
I am having a similar problem with FSL ecept I am not getting an error but I am not getting any statistical output (cluster analysis) but the Image file is being created. I had posted my question before I reposting it again:

I am doing a study involving 17 subjects performing two tasks A and B at two different difficulty levels Fast (F) and Slow (S). Four scans were done with the subjects performing tasks A and B at difficulty level F (x 2 times):
{AF1,AF2,BF1,BF2 (4 EVs)}
and at level S (x 2times): {AS1,AS2,BS1,BS2 (4 EVs)}.

From my understanding of the FSL procedure I have to do a Fixed Effect analysis across sessions first to summate the tasks to generate 4 different EVs:
A(F){summation of AF1 and AF2},
B(F){summation of BF1 and BF2},
A(S){summation of AS1 and AS2} and
B(S){summation of BS1 and BS2}. 

Additionally since I want to compare the difference within subject performing the same task at two different paces I did the following mid-level contrasts using fixed effect to generate two contrast images:
A(F) vs A(S)
B(F) vs B(S)

Thus far I had no problems. I then wanted to do a one-sample t-test across
17 subjects to find out which significant regions are activated during each individual tasks. 

I tried to perform a mixed effect analysis using FLAME 1 using individual COPE files as my input. While I got a statistical output with A(F), B(F), A(S), B(S) across 17 subjects I did not get a statistical output (only image
output) when my input files were the contrast files {A(F) vs A(S)} or {B(F) vs B(S)}. This was not the case when I used Fixed Effect for the higher level analysis as I got a statistical cluster output for all inputs. I had done the same analysis with SPM before and it worked with the GLM analysis there.

My questions for you are:
 1) can I use contrast COPE files like I generated in the mid-level as my input for higher level analysis? 
 2) if I can why does the FLAME analysis not work for these images and only Fixed effect analysis works?
 3) is there a better way of doing this analysis given that I want to see the differences within subject and then do a one-sample t-test across subjects to generate my final result?

Any help from you will be greatly appreciated.

Suman Sen MD
Ruth L. Kirschstein Post-Doctoral Research Fellow
Parkinson's Disease and Movement Disorders Group
Departments of Neurology and Biostatistics
CB# 7025
Univeristy of North Carolina
Chapel Hill, NC 27599
Phone: (919) 966-9281, 843-1474
 
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith
Sent: Wednesday, December 19, 2007 12:09 PM
To: [log in to unmask]
Subject: Re: [FSL] FEAT-Higher level analysis, works with fixed-effects, but not mixed

Hi,

On 19 Dec 2007, at 16:47, Hallvard Røe Evensmoen wrote:

> We have unfortunately run into some more problems with our analysis  
> in FSL.
> Our study gives us 3 different runs from each subject. Each run  
> lasts for
> about 18 minutes, and contains 6 different modes (3 active, 2  
> baseline, and
> pause). From this, we have made 16 different contrasts that should  
> be more
> or less interesting.
>
> We have run all the first-level analysis without any problems.  
> Higher lever
> analysis runs OK with fixed-effects, but when trying any kind of ME,  
> the
> output is always corrupted; we (almost always) get this error:
>
> "ndtri domain error"
>
> Which appears in the log for the higher-level stats, almost in the
> beginning. We have searched the online FSL-forum for help regarding  
> this
> error, but none of the suggestions there helped us. They suggested  
> that the
> first-level analysis could be corrupted, but everything there seems  
> ok. It
> also seems strange that the FE should run if data was corrupted.
>
> To further investigate the problem, we have also tried to analyze the
> lowest possible amount of data, which is one run from 2 different  
> subjects,
> and only one condition (Vanlig-Strek). Still, we get the same error  
> (ndtri
> domain error), and no output. So, we think we can exclude hardware  
> as the
> source of our problems. We have tried different computers, different
> versions of Linux, and different versions of FSL (3.3 and 4.0).  
> Nothing
> seems to help.

Most likely what's going on is that the ME maths is unhappy because  
you have strong outliers in the data, but is doing it's best. Does the  
final output look at all reasonable? Probably the best solution  
(without removing the outliers that is) is to use just FLAME stage 1 -  
does that run ok?

> As a final note, in frustration of all the FSL-errors, we ran the  
> whole
> analysis in BrainVoyager, where it went smoothly.....

Indeed - or just running OLS in matlab probably won't complain  
either ;-)

Steve.


>
>
> Anyone got any idea?
>


---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------

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