Thanks Steve
I will go over all my mid-level analysis to see if there was significant subject o subject variability. I will get in touch as soon as I get that done.
-Suman
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 12:20 PM
To: [log in to unmask]
Subject: Re: [FSL] FEAT-Higher level analysis, works with fixed-effects, but not mixed
Hi - it sounds like your analysis is ok - if you've done all the
within-subject comparisons with a combination of first-level modelling/
contrasts and higher-level FE stats, then you should be set to pass
those COPEs up to a highest-level ME analysis. If the highest-level
works ok with FE then it seems like all the lower-level analyses are
probably ok.
When you did FE at highest-level was the response very strong? Was
there a lot of subject-subject variability? If you have a lot of
subject variability then ME may just not give you a strong enough
response to pass statistical thresholding.
If this still doesn't make any sense then feel free to upload just the
complete highest-level ME output .gfeat directory and we can take a
look.
Cheers.
On 19 Dec 2007, at 17:12, Sen, Suman wrote:
> 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
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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