I agree with Mark, but would also add the caveat that I'm not sure what
you're looking for in the GLM comparison, given that this artificial data
doesn't have the temporal or spatial characteristics of the signal or the
noise in real FMRI activation data? Sorry if I'm missing something!
Cheers, Steve.
On Wed, 26 May 2004, Mark Jenkinson wrote:
> Hi,
>
> This seems quite puzzling and I agree with Joe that you should
> investigate non-cluster-based thresholding to see if that's a problem.
> With zero smoothing in the pre-stats the assumptions of GRF may
> not hold and give you dodgy results.
>
> Also it is worth looking closely at your time-series plots.
> You say that the full model fit doesn't reflect the contrast=2 but does
> the overall shape fit correctly? Can you see if there is a
> mis-specification
> in the model or a problem with the filtering? And what is the
> maximum z value that it finds and is it located in one of your
> artificial
> activations?
>
> I imagine that there is some simple explanation behind this, especially
> as you say you've used it successfully in real data before. If you
> can't
> find the problem though, tar up the .feat directory and put it somewhere
> for us to download and have a look at.
>
> All the best,
> Mark
>
> P.S. Don't email data to the list - put it on a website or ftp site.
>
>
> On Monday, May 24, 2004, at 11:39 pm, Heather Luo wrote:
>
> > Hi,
> >
> > We are doing an empirical comparison between different GLM
> > implementations
> > in three packages: our proprietory NPAIRS, FSL and SPM2 based on a
> > simple
> > simulating image dataset. We sequencially fed the data into NPAIRS,
> > FSL and
> > SPM2. We can see obvious activation blobs in tstat maps from NPAIRS
> > and SPM2
> > as expected, while no obvious activation found in FSL results. The
> > volume
> > correlation R between tstat maps of SPM2 and NPAIRS is 0.64, while the
> > R
> > between FSL and NPAIRS is way below 0.1. We are wondering what is
> > causing
> > such a different result?
> >
> > The simulation data were generated using a 2-slice sub-volume(64*64*2)
> > extracted from a brain mask volume(64*64*32) from one subject for a
> > 1.5T
> > fMRI experiment in which every volunteer was asked to perform two runs
> > of
> > static force task alternating six rest and five force periods/run
> > (44s/period, TR=4s). Four artificial Gaussian blob(FWHM=1, 1.5, 2, 4
> > pixels) activations, each restricted to a 7*7 square, were added to
> > different locations in the second slice. To form the simulated time
> > sequenc,
> > the blobs were then multiplied by the on-off reference function for two
> > parametric static force runs convolved with a Poisson shaped(lamda=7.3)
> > hrf. After adding white noise to the sequence and normalizing the
> > CONTRAST
> > and CNR(CONTRAST-to NOISE Ratio) at the blobs' center to be 2, the
> > simulating data set was obtained.
> >
> > Here is what we did in FSL:
> > 1. avwmerge 120 slices into a 4d analyze image
> >
> > 2. input 4d data into FEAT, high pass filter cutoff = 100, TR=3.98
> >
> > 3. IF pre-stats was included, we used the default pre-stats setting
> > except
> > that we changed spatial smoothing FWHM=0mm
> >
> > 4. in Stats part, we used full model setup, original EV = 1.
> > - Basic Shape: we prepared a text file as custom entry, the file looks
> > like:
> > 00000000111111111100000000001111111111....
> > - Convolution if used: Gamma, phase=0, stddev=3, mean lag=6
> > - contrast: mean, EV1=1
> >
> > 5. in Post-stats, Z threshold=2.3, p=0.01
> >
> > We first ran the data in FEAT with pre-stat and post-stat turned on,
> > we found
> >
> > - no expected activation blobs found in the color rendered stat image
> > in
> > report.html.
> > - from the time series for the voxel with max z, the full model fit
> > doesn't
> > reflect the contrast = 2.
> > - there is no expected high intensity blobs in the unthresholded
> > tstat1.img
> > or zstat1.img
> > (we used a self-developed idl program to view the t/z map, what the
> > program
> > does is to map the t/z score, eg. [-3.9, 4.3] to [0..255] and display
> > the
> > greyscale image. when we did comparison, the t/z maps from NPAIRS and
> > SPM
> > were viewed through the same program as well.)
> >
> > Then we tried again with pre-stat, post-stat, and convolution function
> > turned off, the results are similar as before, no activion blob seen.
> >
> >
> > Heather Luo
> > International Neuroimaging Consortium
> > Minneapolis VA Medical Center
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
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
|