Oh - sorry, forgot to say - your parametric activation in the data
(time-varying height) doesn't fit the model you're using!!
;-)
On Fri, 28 May 2004, Stephen Smith wrote:
> Hi - thanks for sending the data. It looks like you probably ordered the
> data wrongly when you created the 4D analyze file for input to FEAT, as
> your filenames aren't zero-padded. You should use something like:
> avwmerge -t data4d *_?.hdr *_??.hdr *_???.hdr
>
> Melodic estimated one component only in the data, and immediately found
> the activation in the analysed dataset, showing the ordering problem; see
> http://www.fmrib.ox.ac.uk/~steve/ftp/filtered_func_data.ica/report/IC_1.html
>
> Note that this data has quite unrealistic levels of activation (as well as
> noise structure); in the analysed datasets you sent, there is _huge_
> activation, and in the raw data that you sent, the level of activation is
> very low indeed.
>
> Good luck with your study! Cheers, Steve.
>
>
>
> On Mon, 24 May 2004, 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
>
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
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