Hi Smith and FSL experts,
I setup the model and use the parameter according to your suggestion. I
set the thresholding as uncorrected voxel P in 0.1 ( it is very large).
Then I run the FEAT. No voxel is above the threshold. It is very strange
that if I use the SPM to perform the same study, I can set the p value
in 0.05 or below and get a reasonable result. Is there anything wrong ?
Besides, if I have the variance for each image, such as the cognitive
score in controls and patients, how to input the variance ?
Thank for your help
JLH
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Stephen Smith
Sent: Thursday, October 17, 2002 6:27 PM
To: [log in to unmask]
Subject: Re: [FSL] parameter about the group analysis by FEAT
Hi - so it seems like you have only one image per subject, and I will
assume that they are all registered together (if not - you need to do
this). It also seems like you DON'T have variance images for the
subjects.
Therefore there is not too much advantage in using FLAME (the advanced
estimation for group-stats in FEAT) over ordinary-least-squares (ie what
you get if you turned off FILM for first-level anllayses or turn off
FLAME
for higher-level analyses). The only time where you MIGHT get an
improvement with using FLAME is if your two groups have very different
variances. (Note for other people - if you do all your analysis at
first-
and second-level using FEAT then of course, FEAT will pass up parameter
estimates AND variances to the second-level, so FLAME is definitely of
value).
So - in order to input your data into FEAT you probably may as well run
a
"first-level" analysis, according to Joe's suggestions. Start by
concatenating the two 4D files into one by:
avwmerge -t allsubjects.hdr controls.hdr patients.hdr
And then do a first-level analysis with a single EV of 1's and -1's. In
your case you want TR=1 skip=0 OFF=43 ON=7 phase=0 conv=NO
temporalfiltering=NO temporalderivative=NO
contrast 1 (patients-controls) = [1]
contrast 2 (controls-patients) = [-1]
hope this works ok!
Steve.
On Thu, 17 Oct 2002, tulu wrote:
> Dear FSL experts,
> Thanks Joe and Smith for your help. I only have the normalized raw
data
> from controls and disease. So I think I don't have first level time
> series PET data. Dr. Joe, you understand correctly. However I still
have
> the problem in the stats portion. What is the basic shape I should
> choice ? I choice the square and I did not know how to setup the skip,
> off, on, phase and stop after. My data is a 4d analyze format which
1-43
> subject is controls and 44-50 is diseases. Besides, if I need to enter
> the covariance data, how should I do ?
> Thanks your help
> JLH
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Joe Devlin
> Sent: Wednesday, October 16, 2002 11:11 PM
> To: [log in to unmask]
> Subject: Re: [FSL] parameter about the group analysis by FEAT
>
> >Thank for your reply. I only have the experience of " compare
> >populations: 1scan/subject" ( that is a two sample t test) in SPM.
Now
> I
> >have the 2 groups subjects in 4d analyze format. I like to try the
> >"simple" analysis (compared population) and I don't know how to do
it.
> >Please give me any suggestion. Thanks
>
> If I understand correctly, basically you want to compute a two-tailed
> t-test comparing
> patients to controls across the voxels in the brain. I don't see any
a
> priori reason why
> you couldn't do this in Feat but I don't think you want any of the
fancy
> options.
>
> It sounds like you want something like:
> - Put all scans (1 per subject) into a single 4d file containing first
> the
> normals and then the patients.
>
> - You need all of your scans registered into standard space (which you
> can
> do with McFlirt
> if you haven't already done this). Probably, though, it would be best
> to
> do this before using
> Feat because Feat assumes that a single time series comes from a
single
> individual. In this
> case you will enter one time series from many subjects.
>
> - Misc: DOn't change anything here.
> - Data: TR = 1, delete volumes = 0, & you don't want high pass
> filtering.
> - Pre-stats: Turn off temporal filtering here and set the spatial
> smoothing
> to whatever you want (typically 8-16mm in PET).
> Definitely don't want motion correction or slice timing correction.
> May
> not want brain extraction depending on how much
> skull shows up in your PET images. Probably do want some form of
> intensity normalisation but this is slightly tricky (see
> previous email).
> - Stats: Turn off pre-whitening. Select full model setup and create a
> single ev. It should be a set of 1s -- one for each
> normal. Patients will be implicitly modeled. Turn off
convolution,
> temporal filtering and temporal derivatives. The final
> model should look like a column of 1s -- 1 per control followed by
> zeros
> -- 1 per patient. Presumably you want two
> contrasts: Controls > patients (1) and Patients > controls (-1).
> - Post stats: Pick a statistical threshold for accepting significant
> results.
> - Registration: None. Best to do this before creating the 4d data set
> for
> analysis because of the assumptions Feat
> makes -- namely that you're analysing fMRI data rather than pet.
>
> Good luck.
> Joe
>
>
> >JLH
> >
> >-----Original Message-----
> >From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> >Behalf Of Stephen Smith
> >Sent: Wednesday, October 16, 2002 5:18 PM
> >To: [log in to unmask]
> >Subject: Re: [FSL] parameter about the group analysis by FEAT
> >
> >Hi - I'm a little confused by this - are you saying that you have
> >already
> >carried out the first-level analyses from each subject and want to
pass
> >the relevant stats up to second level? Or are you wanting to carry
out
> >the
> >first-level AND the second-level anlaysis inside FEAT?
> >
> >Thanks, Steve.
> >
> >
> >
> >
> >On Wed, 16 Oct 2002, tulu wrote:
> >
> > > Hello Smith and FSL experts,
> > > I try to setup the study. I have one group of controls (N=43) in
4d
> > > analyze format and another groups of disease (N=7). I use the
first
> > > level analysis and number of analysis is 2 ( 2 groups of patients
> ?).
> > > The TR=3, High pass filter cutoff=100. Turn off the FILM
> prewhitening
> > > and turn on the intensity norm. Then the FSL ask to setup model
> >contrast
> > > details after I push the go. Is there any thing should change ?
> Thanks
> > > JLH
> > >
> > > -----Original Message-----
> > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
On
> > > Behalf Of Stephen Smith
> > > Sent: Tuesday, October 15, 2002 10:30 PM
> > > To: [log in to unmask]
> > > Subject: Re: [FSL] parameter about the group analysis by FEAT
> > >
> > > Well - for the first-level analyses the things that spring to mind
> >are:
> > >
> > > Set TR to whatever it effectively was.
> > >
> > > Turn ON intensity norm?
> > >
> > > Highpass - if you set TR "right" then choose A+B length etc?
> > >
> > > Stats - turn off FILM prewhitening and also turn off convolutions
> and
> > > derivatives?
> > >
> > > Let us know how you get on...thanks, Steve.
> > >
> > >
> > >
> > > On Tue, 15 Oct 2002, tulu wrote:
> > >
> > > > Hello, Smith and FSL expert,
> > > > Thank for your reply. Since I am not familiar with the fmri
> setting,
> > > can
> > > > you tell me the detail setting about this particular case ? Such
> as
> > > the
> > > > TR, high pass filter cutoff and the setting in stats ? I will
> share
> > > the
> > > > result if it can work. Thanks
> > > > JLH
> > > >
> > > > -----Original Message-----
> > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On
> > > > Behalf Of Stephen Smith
> > > > Sent: Tuesday, October 15, 2002 7:00 PM
> > > > To: [log in to unmask]
> > > > Subject: Re: [FSL] parameter about the group analysis by FEAT
> > > >
> > > > A scary can of worms - does FEAT work on PET/SPECT? Well - we
> >haven't
> > > > tested it ONCE on PET data, so seems risky to make any
> > > promises.....but
> > > > in
> > > > theory.....should be ok.....
> > > >
> > > > There are bound to be practical issues that come up - will be
very
> > > > interested to see how you get on. The new FEAT5 group stats
stuff
> > > > (FLAME)
> > > > should add value to group stats with PET just like with FMRI,
but
> as
> >I
> > > > said, we've not tested it at all. Your particular case
(N=7/N=43)
> > > could
> > > > well be a good example of when FLAME is better than simple OLS
> > > > (ordinary-least-squares, ie dumb "random effects").
> > > >
> > > > Thanks, Steve.
> > > >
> > > >
> > > > On Tue, 15 Oct 2002, Jung Lung Hsu wrote:
> > > >
> > > > > Dear FSL experts,
> > > > > I have a simple question about the FSL. I have 2 groups of
> >patients
> > > by
> > > > PET
> > > > > study. One is disease (N = 7)and another is control (N = 43).
I
> >like
> > > > to
> > > > > know the difference between the disease group and control. Is
it
> > > > possible
> > > > > to use the FEAT to do group analysis ? If so, what is the
detail
> > > > parameter
> > > > > I should enter in the FEAT program ? Thanks
> > > > > JLH
> > > > >
> > > >
> > > > Stephen M. Smith
> > > > Head of Image Analysis, FMRIB
> > > >
> > > > Oxford University Centre for Functional MRI of the Brain
> > > > John Radcliffe 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
> > > Head of Image Analysis, FMRIB
> > >
> > > Oxford University Centre for Functional MRI of the Brain
> > > John Radcliffe 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
> > Head of Image Analysis, FMRIB
> >
> > Oxford University Centre for Functional MRI of the Brain
> > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> > +44 (0) 1865 222726 (fax 222717)
> >
> > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
> Joe
>
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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